Sunday, February 26, 2017

Week 5

Herry et al. is a notable paper in finding specific populations of neurons within the basolateral amygdala that specifically react to conditioned stimuli both in conditioning and extinction of fear memories. While it would appear that the extinction-related neurons may be inhibitory interneurons, Herry et al. attempts to discredit this by noting that the extinction cells have firing rates comparable to projection neurons. However, this is not backed up by any further attempts to identify the cell types, even ex vivo, which I feel is a significant missing point of information and weakens the paper’s findings.

As has been mentioned in a number of the other write-ups, Courtin et al., while an advancement on the concepts brought forth in Herry et al. and a source of increased specificity with regard to parvalbumin interneurons, was a muddy paper with at time unclear conclusions. Perhaps it was in the language used or the lack of flow and sectioning, but while I was able to follow the general direction of the paper for the first sections, as the paper continued, it became unclear the grand message of the research. However, I personally appreciated the particular attention given to inhibitory interneurons and their disinhibition in conditioned fear expression as opposed to Herry et al. which seemed to avoid local inhibition. Courtin et al. was able to also advance on a number of the ideas from Herry et al., namely in the use of optogenetics in the place of pharmacological manipulations.

Week 5

For the majority of the time that I was reading the Herry et al paper, I was convinced the the two neuronal populations were just representative of two different associations being made with a stimulus (tone) or stimuli (tone and context) and shock, but Fig 6 (along with the distinct connectivity shown in Fig 5) dramatically changed my opinion by showing that BA activity is not necessary for the expression of either the fear or extinction memory, just the switching between the two.

The main question I’m still left with is why there were never any experiments where the animals are returned to the conditioned context and after extinction training. In the same way that they have “Post-FC” data in Fig 1, in which they show that the fear neurons fire in response to tone even in the new context (aka the extinction context), I would have expected a similar “Post-Ext” experiment in which they show that the “extinction” neurons still fire even in the conditioned context (after several trials because this change in context would still induce freezing due to the context-fear association if not the tone-fear association) because they have learned that the tone is no longer associated with shock. Of course, the initial return to the conditioned context would surely cause an increase in the firing of the fear neurons again because of the context-fear association, but Fig 1d shows that these fear neurons are not only responsible for the context associated fear but also the tone associated fear (the animals show freezing in response to tone even in the new condition before going through extinction training) so they should be able to show extinction behavior after some time in the conditioned context.

Just as the animals are able to switch quickly from non-fear to fear states (Fig 4), they should be able to switch from a fear to non-fear state on a relatively fast time scale. Even if it is not as fast as the transition to fear, it should take less than a 24 hour period (the time is takes for extinction consolidation) to switch and therefore prove that it is not a matter of relearning an association, rather it is switching to an already existing one as in the case of the switch to fear after fear renewal. Without this, it is still possible that the BA is necessary for the the acquisition of the extinction and fear memory, if not the retrieval or expression of them, and since this paper focuses on this idea of bidirectional switching between fear states rather than fear-learning or just the rapid switch to fear after extinction, this is an important distinction to make.

I suppose it is still possible that being in the condition context would be sufficient for fear response and that the animals would have to undergo additional extinction training to dissociate the room, in addition to the tone, from the shock but I would be surprised if this were the case since the tone and not the room is the only stimulus time-locked to the shock and therefore should be the main association with fear, and if that association is extinguished, then reduced freezing in the conditioned room after tone fear extinction should be a much faster process.

As for the second paper, it was cool to see a follow up on the circuitry described in the Herry et al paper that showed the upstream modulation of fear behavior by the PVINs in the dmPFC. I feel like I missed something or perhaps didn’t quite understand this paper well enough because I was confused as to how they knew that the PNS are necessary or responsible for the fear expression. Based on what I understand, the PVINs are important because they coordinate the firing of the PNs and it is that coordination that is necessary for the PNs to produce a fear response. Although they show that PVINs activation inhibited PNs and prevents CS+ induced activation and reduced freezing (and conversely disinhibited PNs to increase freezing when PVINs were inhibited), they do not show that the PNs are either necessary or sufficient for fear behavior.

The PNs are 1) responsive to CS tone, 2) project to the BLA which we know to be important for fear behavior, and 3) their synchronized firing is correlated to fear behavior, but I am unclear as to why PN regulation is definitely the cause of the fear behavior and not just a consequence of PVIN activity that is not necessary for fear. As far as I can tell, the PVIN activation and inhibition experiments are not limited to changes in PN activity. Perhaps the key is understanding the cross-correlogram analysis? Or do the PVINs only project to the perisomatic region of PNs? Maybe the PNs being necessary/sufficient for fear behavior is not as important as I am thinking. At the very least, I do agree that the data shows that PVIN inhibition is causally related to and necessary to drive fear expression.

week 5

These papers took on a very interesting topic but were also difficult to comprehend. I find papers that exploring circuitry display the immense intricacy of the brain. I personally saw this especially in Courtin's exploration of synchronization to drive fear expression. Unfortunately, despite being intrigued by the questions both authors were asking and the narrative they were creating, I definitely struggled to grasp much of the content in the paper. There seemed to be an assumption of understanding in the reader and I unfortunately have not come across several of the methods explored in this paper. I am really looking forward to the in-class discussion and  am hoping tomorrow's lesson will fill the missing links and complete these gaps of understanding.

I believe a big question to think about this week is the validity and value of using the classic fear conditioning model as the animal model of choice. All assumptions are made from here. I think this will be an interesting discussion among the class.  I think its interesting to think about in Herry's paper how the extinction neurons are supposed be the neurons of contextualization during fear extinction. Is their activation to US versus the CS enough evidence of their role in the extinction process ? Perhaps with more familiarity with this method of research this would be clear, but although I am convinced they run in a separate circuit than the neurons activating to the CS and not the US, I am still left curious about this assumption. I am also still unsure about their selection and identification of these very small number of neurons. 8-9 neurons just doesn't convince me of much. I liked how in Courtin's paper, to identify their neurons of interest, they first just recorded activity in the area of the BLA, letting the results drive the direction of interest. By identifying the opposite nature of the two subclass of the INs, they were able to further explore the effect of selective inhibition  of the PVIN. To me this a much more convincing method of narrowing down to a few neurons of interest.

Week 5

Of the two papers this week, I enjoyed reading the 2008 Herry et. al paper by far. Having some knowledge of the concepts of extinction and conditioning and the fear circuit aided in my comprehension of the Herry paper, and overall I found it to be very clear and concise. I additionally appreciated how the experiments in the Herry paper clearly followed a logical procession. However, I struggled to understand the 2014 Courtin et. al paper and found it significantly more challenging than papers previously discussed in this class. As many of my peers have addressed, the concept of theta firing and phase resetting was extremely confusing. I had no prior knowledge of this subject, so I have some questions regarding this concept: what exactly is the significance of phase resetting and synchronized firing, and in what other processes is theta firing specifically involved? While I understand the authors likely assumed the readers would have background information regarding the paper’s more abstract topics, I would have appreciated if the authors had elaborated on and reminded its readers of the significance of each finding and its relevance to the original hypothesis. I also recognize that some additional research would help me better appreciate this paper, but after analyzing the research I am still feeling perplexed and overwhelmed by these concepts.

I found the clinical applications of these findings to be exciting because the fear circuit is so heavily involved in psychiatric disorders like PTSD and phobias. Exposure therapy is already one important therapeutic application involving extinction of a fear response that employs repeated exposure to diminish the original fear response. It would be interesting if therapies using optogenetics or electrophysiology could eventually target fear and extinction neurons specifically, either to suppress the exaggerated fear neurons’ response seen in psychiatric patients or enhance the extinction neurons’ activity.

Week 5

During my first co-op I worked as a behavioral therapist serving children with autism and other behavioral disorders. After that experience I have always had an interest in the neuronal processes and brain activity that occurs during events such as reinforcement, punishment and extinction. The 2008 paper was helpful in starting to answer some of the questions I had in regards to the neural networks responsible for these behaviors and occurrences. The Courtin et al. paper was interesting to me because during my second co-op my project involved optogenetic manipulation of parvalbumin interneurons in the visual cortex in mice. While reading relevant literature, I learned that these interneurons had differential and specific roles depending on their location in the cortex. Though interesting, I found the Courtin paper heavy in electrophysiology, which is not my strong suit, so my discussion focus is for the Herry paper.

Unfortunately, I had a difficult time comprehending many of this week’s figures and the discussion of the theta waves/theta resetting. I’ve come across this confusion before, but I still have yet to grasp the implications of the different waveforms on brain activity and neuronal function. I found the 2008 paper the easier of the two to read and get through. I had never taken the time to consider that extinction would be controlled by a distinct population of neurons whose activity opposed a population of fear neurons. I really liked how they addressed the question of whether the extinction and fear neurons could reverse roles – while it’s important to use controls and determine whether the populations were functionally distinct, it was phrased in a way which wouldn’t have immediately come to my mind. I found the flow of the paper as natural, the results of each experiment posed new questions that were addressed in the consequent experiments. This paper absolutely helped me begin to understand the neural mechanisms that are responsible, in part, for extinction.  

week 5

I’m glad I’m not the only one to say this, but like many others, I found the paper by Courtin et al (2013) extremely difficult to follow simply because they addressed various subtypes of neurons, their correlation with freezing, and various oscillation procedures that I am not familiar with. Even though I spent a lot of time trying to dissect and make sense of the paper, I still feel completely lost. Because of this limitation, I was not able to fully understand the depth of research or the take home message associated with it. Hopefully, after tomorrow’s discussion that won’t be the case.

Compared to the 2013 paper, Herry et al (2008) was much easier to follow as their approach was simplistic and I am familiar with the concepts of fear conditioning and extinction. Additionally, their experiments seemed to have a logical flow and seemed to build off each other, which makes it easier to understand. It was interesting to learn about the distinct types of neurons (fear and extinction neurons) and how they represent functionally different classes that have the ability to distinguish between the contexts the animal is in. I also found the concept of emotional perseveration to be quite cool – wish they had more to say about it. Having said that, I was not fully convinced with some of the conclusions made in the paper. For example, in the section titled “rapid reversal of activity during fear renewal’’, the authors found that - After successful recall of extinction memory (Fig. 4b), mice were transferred to the context in which they had been initially fear conditioned. Changing context resulted in a modest, but significant, increase in baseline freezing levels owing to contextual fear conditioning (Supplementary Fig. 3), and in a full renewal of the original cued fear memory. I was a little confused after reading this because isn’t fear extinction carried out in the same context as the one in which the animal was fear conditioned in? So why would they carry out extinction in a different context? Another point in the paper that left me puzzled was - Comparing the averaged time courses of CS-evoked activity of fear and extinction neurons during the acquisition of behavioural extinction indicated that significant behavioural changes occurred after the activity scores of the two populations of neurons crossed over. What do they mean by “crossed over”?

Week 5

Herry et al

I liked reading this study, found it interesting in how it is able to identify two neuron types in encoding fear and extinction. Also interesting to know how these neuron types relationship to other parts of the brain like the hippocampus and mPFC. I wonder though if they could have used more of a variety of fear conditioned stimulus like say an appearance of new object when shocked, it might be redundant but at least you could have more evidence to say it was fear encoding in general not just auditory fear encoding. Overall though again might not be necessary. I would also like to see the specific neurons ablated individually, to see the behavioral results, but since they overlap pretty close to each other it might be to difficult to do right now.

Courtien et al
This paper  I think might be written slightly better than the other paper. Because it focused on a lot of different neuro variables to try and explain extinction and fear learning, whereas the other paper I feel didn't do that as much. I also like that they were able to isolate specific neurons and test it behavioral outcomes which i think is important. If i were to say one thing that i might add is the same thing that I suggested under Herry et al which is to use another CS. I agree with the author that the results of this paper could have important application to disorders that might have a fear component to them.

Herry & Courtin

I got the overall point of the Herry et al. paper, the questions being asked, the methods by which the questions would be answered, and the overall conclusions. However, I couldn’t make sense of a bunch of the figures. Obviously, I knew that figures regarding neuronal activation and how it switches between the fear and extinction neuronal sets were being presented but I often couldn’t quite see how. Right off the bat, the raster plots and histograms through me off and it didn’t get any better from that point on as I couldn’t figure out what the z-score plots were showing. 
Although I had a hard time with the figures, I liked this paper mostly because I agreed with their thought progression. They start off showing the relation between BA neurons and fear and extinction then talk about how the two sets of neurons are different but share the same space and then move on to talk about the circuits these neurons are involved in and how they overlap or don’t overlap in terms of the mPFC and vHip, respectively. They then go on to show necessity of the BA neurons for behavioral changes through inactivation. Overall, I thought this was a well put together paper and I will likely appreciate it even more one I know what all the figures mean.

In terms of the Courtin et al. paper, all I got from it is that they are inhibiting certain neurons and this affect fear expression somehow. Outside of that, I don't know what is going on. I can’t really piece together the big picture of the paper as they just seem to jump right in to their data, or at least it feels that way to me. I definitely have a knowledge void in terms of the details of their experiments. I thought the figures would help, as they tend to do in papers that make sense but, well, they didn’t.