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  • helen 22:09 on March 28, 2015 Permalink | Reply  

    When I said in one of my first posts that I was surprised nerves didn’t look any different to other tissue, I realise I was wrong. Once cleaned, you know exactly when you’re dealing with a nerve, it has a clarity to it that no other tissue has.

    I was initially surprised that I could even see nerves – nerves were things of touch and sensation and purely object-less. I was surprised that my feeling of a soft brush or massage could be embodied in a physical structure – and a clear, stringy one at that.

    I was surprised that a tissue so different to any other in the body wasn’t alive or moving by itself or talking to me.
    Nerves bind things, they animate things and collaborate, yet they are just as much a structure as bone or muscle.

    When I peel away the dried-PVA sheath of connective tissue surrounding the trigeminal nerve, I am about to touch something that makes eyes feel tired and ready for bed, that feels the wakening splash of water to face and controls the chew of a gelatinous treat. But I slip and my forceps slice into the soft neuronal column; detaching string from base and structure from sensation.

  • helen 12:35 on January 22, 2015 Permalink | Reply  

    What is the difference between an internet cable and an axon? 

    I realise that this sounds like the start of a bad joke but it’s a serious thought, here’s what I’ve got:

    • they both carry information, they are just made of different things
    • they are both constrained by physical variables – diameter or degree of insulation for example
    • both can easily be disrupted by scissors
    • axons however, can install themselves.

    Is the crucial difference that wires only exist because axons do?

    I thought of this question as I was sitting in Fabiana’s office. We were trying to load photos of axons from an external location but we couldn’t because the computer’s own axon was not wide enough.

    Perhaps the axon and internet cable are mechanistically similar but it’s the content of their information that makes them different. Show me a cable that can transmit warmth, fear and guilt and then maybe I’ll be convinced.

    Just as I finish typing this, the internet disconnects for a minute and I get scared that my work hasn’t saved. That’s my Ethernet cable politely reminding me that it can in fact transmit fear.

  • helen 21:30 on January 19, 2015 Permalink | Reply  

    some thoughts from the week: 

    For how precise and reliable our neural pathways are, I’m surprised at how messy neurogenesis is.

    Let’s just say that if whoever is responsible for organising the hind brains I’ve seen so far offered to plan my birthday party I would probably say no.

    (That would be a completely different story if they offered to be on decorations though)

    Perhaps I’m just frustrated with not being able to figure out the logic behind the pathways of these dam axons and so scold them for being messy but honestly, you really have to have faith in some of these axons.

    The more I study them, the more I realise just how many of them have no clue what they are doing (that feeling is starting to sound awfully familiar).

    Call me crazy but I have started to characterise/stereotype some of the different axons I see.

    There are the axons that just cling to others for a free ride, or do so because the path seems too daunting on their own, others staunchly travel in their own direction but seem to quickly change their mind and turn back to safer waters.

    I get the feeling that this early, the axons are still so impressionable; they haven’t developed a sense of identity yet, don’t know who they will be serving (the ear? the facial muscles? the chewing muscles? tongue sensation? (If I was ever an axon I would want to be one responsible for taste just personally)

    They all just seem to be on this very tumultuous journey to self discovery and target selection. I wonder if axons that lose their way are the strong, individual ones with their own sense of determination or whether they lose their way because are they aren’t very good at detecting signals from their peers around them.

    Do you think axons ever get nerve envy and wish they were part of another nerve where the target is in a better location, or sends kinder signals?

    And its funny that I am here satirising these cholesterol bound packages, when I really quite literally couldn’t do this without them.

  • helen 16:42 on December 2, 2014 Permalink | Reply  

    As I was talking with Fabiana today, I realised that all this is about is figuring out how something was built – for some reason we both really want to know

  • helen 17:20 on November 25, 2014 Permalink | Reply  

    Here it is! 

    HK012 showing efferents turning and afferents alongside (1)

  • helen 17:13 on November 25, 2014 Permalink | Reply  

    Just had the most exhilarating day in the lab.
    The nerves I dyed yesterday took the stain up beautifully and I got some really juicy (it’s the only word I can currently think of sorry- it’s been a long day) images to analyse. Even though I have seen axons and cell bodies before, the way they dance around each other never fails to inspire me.

    Fabiana joked that she’d find me by the microscope half dead tomorrow morning because I’d been up all night staring at the axons, but she’s only half joking because looking under that microscope does truly transport you to another bubble where everything is developing and looks like the stars. I could be in that world for a long time.

    There is so much intricate detail within each axon and I love that each axon is different, yet reliably structured (apart from a few who just wander off day dreaming). I wish that I could articulate the experience better but it’s truly one of those things that even pictures and words don’t do justice.

    I wonder if when I understand what I’m seeing better (for example. I’ll know I’m looking at efferents, not just beautiful stringy pieces of brain matter), that awe I have for what I see will diminish, but looking at the way Fabiana reacts to the images she sees I doubt that will be the case because it’s still as though she is seeing things for the first time when she looks down the microscope.

    I haven’t quite figured out how to post a photo yet but when I do I will so you can share in at least a little part of the joy I get from looking at these neurons!

    • kubke 22:01 on November 25, 2014 Permalink | Reply

      The marvel has never faded for me. Almost every prep has something special :) For me today it was imagining those axons using their filopodia to poke at each other. I hope I didn’t leave a bruise in your arm in the process of enjoying those!

  • helen 18:43 on November 18, 2014 Permalink | Reply  

    The size of things 

    Today’s lab lesson was on the size of things.

    I guess that’s only natural because the fields of embryology and microscopy are both particularly concerned with the concept of size (is it a concept?). I always find it amusing when I try desperately hard to finely dissect out the heart or the rhomboncephelon and then I take it outside of the petri dish and onto a tissue where I look at it macroscopically and it’s the tiniest piece of sludge.

    To me at least that’s what it looks like, but I know deep down that it is much more structured and complex than that. That is then further confirmed when you look at things on the precious Nikon microscope and realise that the nerve itself isn’t small, the axons of the individual neurons are.

    It makes me wonder how narrow our ability to perceive things is, based on our spectrum of visible light and the ‘zoom’ we have. I wonder how many things I take for granted as being just a piece of sludge when really it’s an intricately developed organ.

  • helen 15:16 on October 30, 2014 Permalink | Reply  

    Very happy to have found out that I will be continuing my embryology work over the summer with Fabiana through a University of Auckland funded research studentship!

  • helen 07:05 on September 18, 2014 Permalink | Reply  

    Student in the lab week 2 

    We were back in the lab this week but on a different microscope – a beautiful Leica. My only previous experience with the brand had been staring in the cabinet at their beautiful cameras whose price made you cringe slightly. This little red logo made sure to tell me I was working with some high quality lenses, it was a little intimidating I have to admit.

    The optics felt different this time and they were, different lens colours could be put on to give this underwater world a different tinge. We placed the dish on the microscope plate and the image came up on a computer screen. The embryo this week was much smaller than the previous two I had worked with, it bobbed about like a rubber duck in a bath or a seat on a carousel.

    Today was very much a directed session with Fabiana taking the ropes and leading me through the dissection. It was important to be able to make the little clarifications – that’s the notochord right? “no that doesn’t exist” or “you can’t see the trigeminal in this view but I’ll get it in view for you now”

    I realised just how much this imaging was a light-game, and instead of thinking that I’m seeing all of the structures that exist, I need to realise that I am only as good as the illumination of the body, and that most of the time I am not actually seeing structures, but the shadows that they cast.

    My main question of today was ‘where are the nerves? I want to see these nerves’ and it surprised me (although looking back on it now my assumption seemed irrational) that there was nothing distinctive about the nerve tissue.

    I think because nerves seem like the holy grail of all tissue, for some reason I assumed they would look different to other more mundane structures. It’s like I expected them to be shiny or sparkly or something!

    The hierarchies we place on different tissue is interesting, I think nervous tissue is more precious than muscle and muscle more interesting than bone, but does everyone think that?

    I have a feeling I’m going to become a bit of an ectodermal snob throughout this project (Fabiana openly acknowledged she is). We can both tolerate a little mesoderm, endodermal tissue on the other hand we can’t stand!

  • helen 20:03 on August 22, 2014 Permalink | Reply  

    Hi, H here, the newest addition to the lab. I’ve got to say, I am overwhelmed by the receptiveness and kindness I have received from the uni research staff (one researcher in particular whose name starts with F) who have welcomed me with open arms and made me feel completely at ease. The fact that I can send an email to someone and find myself trusted to dissect an embryo in their lab just three months later reminds me what a great education system I am in.

    Although there are many things I could discuss here, I’m going to focus on the thing that has stuck with me most this week and that is the act of dissection. Taking apart a tiny little life system that is a chicken embryo is an incredibly visceral experience. What makes it so interesting is that on one hand you are dealing with concepts of (what was) life in its most precious and potential form but on the other hand these all manifest in the reality that is tissue that can be torn and destroyed by the smallest of movements.

    I remember first seeing the mid brain (a big bubble of tissue on top of the embryo’s ‘head’) and thinking how wonderful it was that it was lined with a large population of baby neurons, but all I really wanted to do was pop it. This was tissue that was going to go on to do great things and all I wanted to do was put my forceps right through it and make it burst like a water balloon (and that’s exactly what we did when we pinned it to the dish with the tiniest little pins I’ve ever seen).

    A similar experience was peeling back what would have gone on to become a spinal muscle like it was pva glue that had dried on my hands, or pressing down on the heart and watching blood float out in a small tear in the ventricle.

    When all the theory and conceptual stuff intersects with the reality of tissues and organs, you get an interesting juxtaposition that can’t help but re-shape how you view concepts of life and growth.

    All I can say is I’m excited to keep learning how to find my way around these embryos!
    Bring on next week ☺

  • 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!

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