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Draft #6, week 12, notes on the male reproductive system

Submitted by vvikhrev on Sat, 04/14/2018 - 13:12

machinery produces gametes = testes
testis histoligcal picture, seminiferous tubules, each lobule has a single one of these, connected at the end, single piece
spermatogenic wave seen at different cross-sections of these STs
picture (label testis)
immature gametes but those at the bottom are sertoli cells
req’d for sperm maturation/production
dev of speratocytes into spermatids (mature towards the middle but not functional yet)
cells in the ISF
Leydig cells, have LH-receptors to make testosterones aka leydig make test in response to LH
sertoli cell has FSH-receptors, makes inhibin then NF effect that feeds on pituitary and hypo
blood testis barrier, how do the premordial germ cells get thru it
fluid in ST is different from serum (that’s how we know it is a barrier, active transport)
primary germ cells become spermatoccytes then ...

test can be converted to 2 horomes 5 alpha DHT and
reductase does this, when it is converted into this, ir can’t be reconverted, it becomes an androgen
araamotase converts testosterone to estragen
is testosterone acting via androgen that hits the androgen receptor or estrogen that hits and estrogen receptor?
androgen receptor that mediates effects of DHT
DHT is responsible for some thing in the male
test and DHT and how the receptor works
can be converted to DHT depending on the cell
test receptor is not bound to DNA, test binds to it, dissociation of HS protein and translocated to bind to DNA and regulate transcription of genes
that is why DHT and test can produce different effects, different chromatin sites = different genes and that is how they are different and are able to tell the difference

Draft #5, week 12, 3 hypotheses on depolarization in the RGCs

Submitted by vvikhrev on Sat, 04/14/2018 - 13:10

3 hypothesis on why when surround-illuminated you are releasing less Glu and you are hyperpolarizing these cells that some how leads to depolarization of cone center presynaptic terminal membrane
1.) GABA hypothesis:
center + surround = less GABA released = less inhibition becomes horizontal cells become more hyperpolarized by surround cells
so if you give exogenous GABA, it blocks depolarization, abolishes the response
not just local when you do this so it can be changing input resistance of the whole membrane (explains suppression of HC feedback sys)
adding charged cations is equivalent to depolarizing charge on the inside and might inibit cahnnel opening and reducing NT release
if this is correct you would expect finding a lot of open hemi-channels (1/2 gap junctions), not found in mammals
if you block these channels, you can suppress horizontal feedback (but you don’t know if it’s affecting just local synaptic region, could effect other VG-channels)
use blocker and you don’t see block of these gap junctions
if you get rid of these channels (lacks connexin), you can reduce but not eliminate CS LH
if you knock it they can go to a different compensatory change
can contribute but not the only mechanism
3.) pH hypothesis
release protons, artifically acidify/alkanize cleft you can account for horizontal feedback, has an effect
block-it clamps pH, changes in proton release can’t change pH and block feedback
show-it, have fish express reporter of pH (GFP) you get changes in pH in predicted region
timing of pH and magnitude changes at the right time, CS illumination and place

Draft #4, week 12, regulation by a LCR notes

Submitted by vvikhrev on Sat, 04/14/2018 - 13:07

- 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
- sequence comparison of the mouse and human genomes revealed a 2-kb homology (H) region far upstream of the MOR28 cluster
- negative feedback regulation ensures that one receptor-one olfactory neuron rule in mouse
- attachment of the H region to the truncated YAC constructs restored the expression of all the transgenes in the cluster
- crossed it with the transgenic that they made and found that they don’t express the same cell = its monoallelic, the LCR is intact

Draft #3, week 12, Sjogren's Syndrome study figure analysis

Submitted by vvikhrev on Fri, 04/13/2018 - 09:32

What is Sjogren's syndrome? (also known as SIcca's syndrome)
It is an autoimmune disease that affects the various organs (pancreas and the liver) and causes severe dryness in the mouth and eyes. There are various studies on this disease but scientists are still trying to figure out the genetic causes (and/or environmental). A study done in 2013 by Christopher J. Lessard looks at "variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren’s syndrome." The contributors to this study formed some type of database to contain all the information about the disease in one place along with the various case studies.
There are 6 figures in this study display the information of the genotyping of both controls and people that exhibit this disease. The figures show the data in various ways. Figure 1 is very neat and easy to read with minimal colors (black and white) and only pointing out the important things that stood out with some red color. Figure 2 contains 6 images of graphs that display the zoomed in data with more detail that was pointed out in red in Figure 1. Table 1 is a little difficult to read because there are no grids separating out the numbers so it is hard to distinguish the columns and rows. Figure 3 has 9 images of statistical graphs that are all the same color therefore it is not as visually appealing. I am sure that if they had to make a poster they would have made each graph different colors so they stand out more and don't all blend together. Table 2 looks just like Table 1 therefore it is also hard to read. Same thing goes for Table 3
This quick figure analysis has helped me sort out some things not to include on the final poster. Even though I am only comparing the final poster project to a paper, it still provides some insight on things that look good and things that don't

Draft #2, week 12, female reproductive system notes

Submitted by vvikhrev on Fri, 04/13/2018 - 09:04

hormonal cycle and ovarian cycle are related
H derived from growing follicle in ovary
growing follicle produces hormones
ovulation = the big spike in LH
estrogen v progesterone graph
thickness of uterus, needs strogen as primer and progesterone increases the endometrium of the uterus
estrogen causes synthesis of prog receptors, no estrogen = no prog
estrogen has proliferatice effect

ovarian cycle, primary follicles grow under FSH (FSH causes them to grow)
LH causes ovulation itself
LH then causes glutimization of corpus lucium that remains in the ____
corpus ludium produces prog, req’d fo ruterine lining for pregnancy,
no progesterone = corpus involutes and creates scar tissue

follicles all present at birth, set at fetal growth, grow in response to FSH
inc in granulosa cells, thecal cells
hostilogical prep of oocyte image
folliculum epithelium is the granular cell
thecal cells outside of granulosa cells (internal and external types)
thecal cells are making steroids
LH stimulates estrogen production from thecal cells
FSH stimulates granulosa cells and LH stimulates thecal cells*** to make hormone

Draft #1, week 12, proposal abstract final paragraph

Submitted by vvikhrev on Fri, 04/13/2018 - 09:03

Our proposed research question is: How does microinvertebrate soil diversity vary with proximity to trees, water sources, and buildings. Groups will collect soil samples at varying distances from these three variables, then count and identify the species present. Information obtained from the soil samples will help in quantifying species diversity and soil diversity. Species diversity is an indicator of tree and soil sustainability that will provide data for future tree and soil management and be beneficial to the UMASS Amherst campus local climate.
Our proposed research question is: How does microinvertebrate soil diversity vary with proximity to trees, water sources, and buildings. Groups will analyze soil samples collected at varying distances from these three variables, then count and identify the species present. To extract soil dwelling organisms from the samples, groups will use Berlese funnels. The information from each soil sample will help in quantifying soil diversity and provide an understanding of the UMASS campus’ environmental sustainability.

Draft #2, week 11, the digestive system part 1

Submitted by vvikhrev on Fri, 04/06/2018 - 14:35

Blood Flow in the GI tract -
- aorta branches off mesenteric arteries that go into the intestins and spread along muscle bundles, into the intestinal viilli and into submucosal vessels under the epithelium to serve the secretory and absorptive functions of the gut
- during digestion, vasodilators are released, mostly peptide hormones like CCK, VIP, gastrin and secretin
- oxygen [ ] decreases in order to increase intestinal blood flow
Mitosis of differentiated intestinal cells accounts for much of the replacement, ~3 days -
- radiation causes a lot of harm to these cells b/c they are rapidly dividing
- countercurrent mechanism of the villis: arterial and venous flow, opposite directions and right next to each other allows for blood O2 diffusion ot of the arterioles into the adjacent venules w/o being carried in the blood to the tips of the villi
EX: during GI diseases, villi become damaged, leading to greatly diminished intestinal absorptive capacity
- also allows for rapid absorption of things going in and out of the liver
- stomach: storage, mixing and emptying, peristalic waves = “pyloric pump”
EX: gastrin increases activity of peristalic pump promotion of emptying of the stomach because it secretes highly acidic juice which stimulates motility
- note: pancreatic enzymes become active only when they come into contact w/ the acid in the chyme
- stomach “pseudo-sphincter: processes food, communicates w/ duodenum to control chyme transport
- when fat enters the duodenum, hormones (CCK) are released, and bind with receptors on the epithelial cells, CCK inhibits pyloric pump and increases pyloric sphincter strength contraction (fats are slower takes longer to digest)
- CCK then inhibits stomach motility that was initially caused by gastrin
- other inhibitors inc. secretin released from the duodenal mucosa in response to gastric acid that came from the stomach
- inhibitory hormones inhibit stomach emptying whn a lot of chyme (esp, acidic and fatty chyme) has entered the duodenum
EX: what do proton-pump inhibitors do to the stomach? – decrease acidity in the stomach leading to decreased functional ability of the duodenum
Mixing contraction in the SI -
- distension causes local peristalic contractions that are segmented in the SI
- promotes mixing w/ secretions in the SI
- even tho it is slow waves in the SM that cause segmentation contractions, these contractions are not as effective w/o other excitation, esp. from the myenteric nerve plexus
¬ caused by electrical slow waves – 12 contractions/min, 1cm
Propulsion -
- chyme is propelled thru the SI by peristaltic waves, slow from pylorus iliocecal valve
- peristaltic activity is increased by “gastroenteric reflex” that is initiated by stomach distension and conducted primary by the myenteric nerve plexus from the stomach to the SI
- but ALSO HORMONES – gastrin, CCK, insulin, serotonin enhance motility and are secreted at certain times
- but secretin and glucagon inhibit SI motility
¬ caused by peristaltic waves – 1cm/min, 0.5-2cm/sec

Draft #1, week 10, in-class notes on posters

Submitted by vvikhrev on Fri, 04/06/2018 - 14:33

Today in class, we went around Morrill and visited several posters and "graded them". It was an interesting activity and has given me a better idea of what details are important and which aren't, what designs to have or not, and the rest of these factors:
- word count
- organization
- emphasizing key information
- flow
- spacing
- color scheme
- sections (title, abstract, intro, question, references, results, methods and materials, summary)
- font size

The poster should have a nice design and be nice to look at. This includes, contrast, balance, spacing, consistency in figure and color arrangement. Consistency is very important!! For example, the red over here means the same thing as the red over there? Pick the best font and size. Make sure organization roles are fulfilled and stay on track with the instructor's requirements and organization guidelines. Do you need both an abstract and an introduction? if you want your poster to stand alone then it is a good idea to have both. If you will be next to your poster the entire time then an introduction is sufficient. Create a concise flow. Do you need to label your figures? Make sure to upkeep expectations.

Week 10, Perfect Paragraph

Submitted by vvikhrev on Fri, 03/30/2018 - 11:02

When I had to think of the significance that the research my group might conduct, I thought about what is already known about the UMASS campus, including its reputation, its goals, and the possible potential of this university. If sustainability and taking care of the environment is something that UMASS strives for and cares 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 climate" is actually paying off and worth it. For instance, if you look at all of the trees on this campus, you can tell how much work has been put into managing them. 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 because species diversity is a great indicator of sustainability. Sustainability is important for the college campus.

Draft #6, week 10, Hofmann Ch. 14 notes

Submitted by vvikhrev on Fri, 03/30/2018 - 10:57

- a successful proposal and grant application is key to pursuing your research
- "your proposal must establish a connection b/w your project's goals and the agency's philanthropic interests" (pg. 205)
- you basically have to kiss-up and try your best to be the best because there is always competition and you need to stand out
- follow instructions exactly and concisely
- if there are no instructions provided then include the following: Abstract, Background (inc. statement of need). research design, significance/impact and should answer these questions: Why this project? Why you? Why at your institution? Why this sponsor? Why now?
- the abstract should highlight all of the other sections, the first sentence is a lot more important that you think and it needs to be concise, informative, and complete
- do not forget your statement of need
- in the introduction/background include the background, statement of need, and the hypothesis is optional (don't overdo it)
- the research design must include the rationale, experimental design analysis, expected results, but alternative strategies are not always needed
- the significance/impact section should be one paragraph, focusing on the benefit your research would bring to field and society


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