vvikhrev's blog

I believe that it can sometimes be difficult to come up with the significance or impact that your research will provide. This is because you can't predict the future of science. However, one thing you can know for certain is that your research (if valid) will give other people something to think about and maybe use for their own research, like a continuation of your research. Your research can provide that foundation for future breakthroughs and can also possibly teach something to young scientists that are out there.
When I had to think of the significance that the research my group might conduct, might bring. I thought about what is already known about the UMASS campus, including its reputation, its goals, and the great potential this university has. If sustainability and taking care of our environment is something that UMASS strives for then this kind of research can provide some kind of data to management facilities, students, and research facilities. This information can include not only ways to create a sustainable environment but also a means to evaluate whether or not all of the hard work that people have put into the campus micro-climate is actually paying off. For instance, if you look at all of the trees on this campus, you can tell how much work has been put into managing these campus trees. However, it is important to ask yourself if it was all worth it? What kind of benefit does it bring to our society? Is it sustainable for the present-day and more importantly, for the future? Our research can provide some kind of feedback on that by measuring biodiversity/species diversity in the soil around various campus trees. Species diversity is a great indicator of sustainability.

- the LCR was first identified and characterized in Globin genes
- in the human visual system, an LCR has an important role in choosing either red or green opsin in a mutually exclusive manner
- each cone expresses only one pigment
- an LCR stochastically chooses one of the 2 promoter sites of the red-green pigment locus
- the physical interaction b/c the promoter and LCR activates the transcription
- b/c the red and green pigment genes are located on the X chromosome next to each other, this mutually exclusive acivation alone ensures monoallelic expression, you get equal # of red and green cones b/c its random, randomly interact w/ the 2 promoters
- monoallelic because it is on the X chromosome (cells randomly inactivate X), this is why males are more likely to be colorblind
- there is positive and there is negative LCR regulation
- since these notes are on the Olfactory Receptor cell and the rule how one olfactory neuron has one receptor, I will talk about positive regulation in regard to Olfactory Receptor gene expression
- structures of the transgenic and endogenous MOR28 genes (make two mice and cross them together)
- the transgenic MOR28 (Tg B6/lacZ) has a C57BL/6 background and is tagged w/ tau-lacZ
- put reporter at the end of the gene, a way of looking at where the gene is espressed, adding a gene
- the endogenous MOR28 (129/GFP) has a 129/Sv background and is tagged w/ gap-GFP
- GFP was introduced into the 129/Sv background by the knock-in method
- this shows that there is monoallelic expression of the odorant receptor gene and axonal projection of olfactory sensory neurones

DNA recombination -
- an example of gene translocation is the antigen receptor gene in the vertebrate immune system
- in B lymphocytes, DNA recombination (aka VDJ joining) leads to the expression of one particular variable (V) region gene for each
immunoglobin (Ig) light- or heavy-chain gene
- in the Ig k light-chain genes, there are >300 germline V segments and one constant (C) gene locus containing 4 joining (J) segments
and an enhancer region
- once the B cell has picked its AB, it proliferates many clones of the same antibody and we can fight off the immune attack
what are variable regions, it is random
- in the chromosome in the B cell, this is where its happening, a permanent excision of this part of the DNA
- the ones that aren’t good, die
- promoter sequence and enhancer (drives expression, in the intron, between variable and constant domain)
- DNA deletion brings a promoter carried by each V gene segment and the enhancer region b/w the J and C gene segments into
proximity, thus activating the translocated gene
Gene Conversion -
- this is another gene-translocation mechanism that activates one particular member of the multigene family (found in yeast mating-type choice and antigenic variation in African trypanosomes)
(- chicken Ig and T-cell receptor genes use gene conversion for their expression and diversification)
- the cell makes a copy of the gene and inserts it into an expression casette
- a copy of the gene to be activated is transferred into the expression cassette located remotely from the gene cluster

How do individual OSNs that express a single type of odorant receptor (OR) converge onto the same glomerulus in the OB
- odor info is detected by ~1000 different olfactory epithelial ORs and this is topographically represented by the ~1000 pairs of glomeruli in each OB
HOW is this target precision achieved??
Mouse
- ~1000 functional OR genes in the mouse, comprising 4% of all protein-coding genes in the genome, are dedicated to olfaction
- largest multigene family in mouse
- OR genes are clustered at ~50 different loci that are scattered among most of the chromosomes
- “one neuron – one receptor” rule = one allele (paternal or paternal) per neuron
- the OR gene choise in mouse appears to be stoachastic (one allele)
HOW is it that a single OR gene is chosen and activated from a repertoire of 2000(3000)?
What kind of mechanism would be possible to maintain the expression of only a single OR gene in each OSN??, these are the possibilities:
1.) DNA recombination
2.) gene conversion
3.) regulation by a locus control region (LCR)

This is what I need to study for my next exam:
SLEEP – CIRCADIAN RHYTHMS
Circadian rhythm –
1. Fluctuations in alertness, energy and mood over the course of the day.
Biological clock: ~24 hr period
2. These shifts are related to underlying bodily processes
Daily cycles occur in: hormone production, body T, blood pressure
3. Changes as we get older
EX: we don’t wake up as early now as we used to as kids
4. We seem to function better (both cognitively/ physically) in our peak time:
MEQ = “morningness eveningness questionnaire”
- college studens are mostly neutral&evening
- adults over 60 = 80% morning
5. Our circadian cycles run a little bit long. We see evidence of this in: Jet Lag (it is difficult to go from east to west), Monday morning
blues
Why Do We Sleep?
Nobody really knows, but here are a few theories…
1. Sleep provides some essential biological function
- Evidence: make up lost sleep, sleep deprivation effects: moody/irritability, mental work suffers (major accidents), immune system,
sleep debt, etc
- Problems with this theory: the amount of sleep any individual needs varies,
motivation can overcome cognitive deficits (like money),
too much sleep increases mortality rates (7-8 hrs optimal, 10 hours = 2x
as high mortality rate)
Paradox: when allowed to free-run, people sleep 9-10 hrs/day

For the research proposal, our group wants to look at microclimates in the soil under various trees on the UMASS campus. There is very few research on the microclimates present under trees on the campus. Some research states that natural forests have greater invertebrate diversity than managed trees (https://www.sciencedirect.com/science/article/pii/000632079500015V). However, since all of the trees on campus are considered “managed” we will not be considering this factor in our prediction. Other research suggests that ants are great ecological indicators of the microclimate found in the soil under trees (https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/1540-9295%2...) therefore ants will be one type of invertebrate that we are going to consider when measuring diversity under various trees across campus. Other research uses invertebrate diversity as a indicator of sustainability however invertebrates are not known as well and are too diverse to create a proper report. (https://link.springer.com/article/10.1023/A:1013397410297) “In ecology, sustainability (from sustain and ability) is the property of biological systems to remain diverse and productive indefinitely. Long-lived and healthy wetlands and forests are examples of sustainable biological systems. In more general terms, sustainability is the endurance of systems and processes” (Wikipedia). The sustainability of the tree could be measured by collecting/recording the species diversity and comparing it to other trees on campus. Some factors we can consider are: the distance of the tree from the road, from a body of water, the diameter and height of the tree and which side the tree is facing the sun vs which side isn’t.

In response to this week's assignment, I took an introductory to statistics course during the Spring of 2015. It was set-up as a team-based learning class therefore towards the end of the semester my team had to complete a large research writing project. This project encompassed all of the concepts we learned throughout the semester. Other than that, basic statistical concepts that I do remember learning were mean, median and mode. I also learned a lot of survey-taking approaches and then how to incorporate the survey raw data into some type of graph. I remember learning about possible graphical skews and biases that might not be noticed at first glance. It was a great learning experience overall, considering how bad I was at AP Statistics in high school. This type of knowledge became very useful in my science classes.

just to review for my upcoming exam, hear are some notes:
There are 2 theories as to how our brain perceives sound. (the brain detects pitch!!!)
1.) Frequency theory: the frequency of auditory neural impulses corresponds to frequency of tone. lower notes vibrate at slower speeds and higher notes vibrate at higher speeds, as pitch increases, nerve impulses of the same frequency are sent to the auditory nerve
EX: a tone with a frequency of 700 Hz will produce 700 nerve impulses per second
- it is speed that determines pitch!
2.) place theory: we can hear different pitches due to sound frequencies on specific parts of the cochlear basiliar membrane, different parts of the cochlea are activated by different frequencies
EX: a sound that is 6000Hz would stimulate the spot along the membrane that passeses a characteristic frequency of 6000 Hz
- the brain detects pitch based on the position of hair cells that transmitted the neural signal

There are 2 theories as to how a "taste is encoded" by taste receptor cells
1.) Labelled-line model: each single TRC can sense all 5 tastes but it will only respond to one, they are innervated by individually tuned nerve fibers
2.) Across-fiber model: has two parts: individual taste receptor cells are tuned to multiple tastes and the same afferent fiber carries info for more than one taste OR that TRCs are tuned to single taste qualities but the same afferent fiber carries info for more than one taste

There are 3 theories/models to the mechanical gating of touch
1.) Indirect/Direct tether model
2.) membrane model
3.) secondary-messenger model

https://goo.gl/images/siQGpz

Since Chapter 5 was on data presenting, I thought it would be interesting to share this image. This is a great and appealing visual display of their  data. I don't think there could have been a better way to display it!

This is a link to how intrinsic our hand is. There are so many nerves in our hands, with different sizes of receptive fields and cortical representations. Here is an interpretation of the figure: 

     EX: motion sensitive neuron responds to stroking the skin in all directions

     EX: direction sensitive neuron responds strongly to motions towards the ulnar side of the palm but fails to respond to motion along the same               path in the opposite direction

     EX: an orientation sensitive neuron responds better to motion across a finger (ulnar-radial) than to motion along the finger (distal-proximal)                 but doesn’t distinguish from radial nor proximal from distal directions

displacement of hair bundle to taller SC inc. # of open channels, producing an increase of inward resting current deploarizing voltage change = receptor potential inc. permeability to (+) dep more NTs released
at high tone bursts, rate decreases b/c fiber is adapted and less likely to respond
How can the auditory nerve signal the large range in level of audible sound from 0-100 dB? (b/c when theres masking fiber can’t signal changes in tone burst)
1.) as the level of tone increases more and more fibers that are tuned to other CF begin to respond, b/c tuning ccurves become broader at higher sound levels
2.) auditory nerve fibers vary in sensitivity to sound and as sound level is incresaed, the less sensitive fibers begin to respond

Phase-Locking: when neurons only fire at a preferred phase of the sound wave at each cycle, usually at peak amplitude
- phase-locking in nerve fibers results from the phasic release of NT as dictated by the ac receptor potential
- @ low frequencies, neurons can fire APs at every cycle, easy to determine frequency of sound b/c it’s the same as the frequency of the neurons APs
- @ higher frequencies (1kHz-4kHz), neurons can’t fire AP w/ every cycle, b/c firing rate is limited by refractory periods
- the only code for sound frequency at high frequencies is the place code
- intensity of stimulus is encoded by the # of fibers that are active other than frequency of firing

The relationship between degree of bundle deflection and receptor potential magnitude is neither linear nor symmetric
I.E. – displacement of bundles in the depolarizing direction produces larger response than equal displacements in the other direction = sigmoidal input and output (not sine)
Thus, symmetrical sinusoidal deflections of the bundle (as might occur with acoustic stimuli) will produce both (ac) and (dc) changes in membrane potential.
dc Component = superimposed depolarizing steady-state
ac Component = sinusoidal
- as you increase F, there is less of this but dc component will remain unperturbed (this is called rectification)
OHC: function to amplify the signal so there is a high sensitivity to hearing
- decrease in resting length by a factor of 4 from the apical to the basal ends, responds by altering its length
- there is a driving force to hyper- and de-polarize the cell depending on K+ and Ca2+ channels
- depends on ratios of ion channels and capacitance of the membrane, there are also big and small hair cells, EX: bigger hair cells respond better to lower F