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Topics in Plant Bio Notes

Submitted by samihaalam on Mon, 10/23/2017 - 00:02


  • large gametophytes, small sporophytes 



  • sporangia = where meiosis produces spores


  • antheridia = male sex organ, produces sperm
  • archegonia = female sex organ, produces eggs
  • water needed for reproduction in bryophytes - sprem need to swim to egg
  • moss

Vaascular Plants:

  • small gametophytes, large sporophytes
  • sporophytes become more dominant than gametophytes maybe because diploid more resistant to deleterious mutations
  • still need water for sperm to swim to egg
  • ferns


  • heterospory:2 different types of spores!
    • microspores: give rise to male gametophytes
    • megaspores: give rise to female gametophytes
    • come ferns, some lycophytes, all seed plants!
  • young, 2n, multicellular embryo stays inside megagametophyte instead of young zygote attached to gametopyhte
    • some ferns and lycophytes
    • prelude to seeds

Comm 118 Study Guide Exam 2

Submitted by samihaalam on Sun, 10/22/2017 - 23:52

4 Types of Address Terms:

  • T = title
    • Mr., Mrs., Ms., Doctor
  • LN = last name
  • FN = first name
  • NN = nickname

based on:

  • kind of name
  • context
  • relationship
    • symmetrical use: both use FN, both use LN, etc
      • maybe both use LN in sports team, etc
      • is there a situation where both use T?
    • asymmetrical use: you use FN, they use T, etc
      • student, teacher relationship
      • some Asian communities need to know ages, etc

when do you move from FN to NN? when do you move from LN, or T, to FN?

  • markers of relationship phases
  • communicates closeness
  • relative closeness, equality


CLV3 cycle

Submitted by daniellam on Sun, 10/22/2017 - 23:40

CLV3 prevents stem cells from continuing to proliferate beyond their limits. It does this by interacting with WUSCHEL, another gene that allows stem cell proliferation. CLV3 works as negative feedback to inhibit WUS. Xu and his colleagues were able to mutate the CLV3 to allow the tomato plants they were working on to increase its fruit size. In their experiment, they used clv3 mutants: fab (fascinated and branched) and fin (fascinated inflorescence) mutants; these mutants have enlarged meristems that produce more fascinated shoots, more leaf primordia and branching, and extra locules (Xu 784-785). They made null mutants, which do not have an effect on the mutants, of SlCLV3 (tomato homolog of CLV3) and observed the high upregulation of the peptide in the clv3 mutants (Xu 788). This means that CLV3 does have a role in regulating meristem stem cell proliferation as the population of stem cells increase. The modified SlCV3 was seen to rescue the fin seedlings from overproliferation and showed to reduce the meristem size to one similar to the wild-type plants (Xu 787).

Xu, Cao, et al. “A Cascade of Arabinosyltransferases Controls Shoot Meristem Size in

Tomato.” Nature Genetics, vol. 47, no. 7, 2015, pp. 784–792., doi:10.1038/ng.3309.

Cell and Molec Notes 10/17 Part 2

Submitted by samihaalam on Sun, 10/22/2017 - 23:13

Fig 1:

  • co-localization = where things overlap in cell
  • used pulse-chase methods!

MC vs PC:

  • MC = Manders overlap coefficient 
    • # voxels with above-threshold fluorescence in 2 channels / # voxels with above-threshold fluorescence for 1 of the 2 channels 
    • MC of LDLR with clathrin = how much LDLR-pos voxels that also contain clathrin
  • PC = Pearson product-momentum correlation coefficient
    • normalized covariance in fluorescent intensities b/w 2 channels 
    • range from -1 to 1
    • 1 = 1:1 correspondence in intensities
    • 0 = 2 intensities uncorrelated
    • -1 = 2 intensities are inversely correlated
    • expect to see covariance if 2 components related stoichiometrically
  • changes in MC and PC indicate change in association
    • when 2 components begin to interact, MC and PC both rise
    • when 2 components being to dissociate, MC and PC both decrease 
  • PC better measure of dissociation than MC


  • co-localization of LDL with lipoprotein
  • 4°C = temp where things can bind, but not necessarily be taken into the cell
  • MC LwR = MC of LDL with LDL receptor (LDLR)
  • MC RwL = MC of LDLR with LDL
  • PC of LDLR with LDL
  • → why no PC of LDL with LDLR?
    • because that's the same thing - it's measuring stoiciometric ratio
  • → why does MC LwR differ from MC RwL? 
    • because one case is how much LDL positive stuff also contains receptor; other is how much receptor positive stuff contains LDL; different things!
  • MC LwR > MC RwL > PC
  • PC at about 0.58 - but from 0-1? is it because it's normalizied? does that mean  0.5 on this scale is really 0, 0=-1, 1=1? 
    • assuming 0.58=0.58, means the two are kinda related stoichiometrically? related at a 1:0.5 ratio? (AKA 1:2?)
  • MC LwR = 0.85, MC RwL = 0.7
    • relatively high association of LDL with its receptor, they're near each other often times? 

B: MC and PC for LDL receptor-clathrin colocalization - how often LDL receptor and clathrin are found together

  • clathrin coated pits - clathrin is on pits, signals endocyotsis to happen when things bind to their receptors!
  • MC RwC = MC of LDL receptor with clathrin
  • MC CwR = MC of clathrin with receptor
  • PC of LDLR with clathrin
  • all in presence or absence of LDL
  • MC RwC goes down slightly in presence of LDL - all the R voxels that also contain C
    • LDL causes R to not associate with clathrin as much?
    • kinda makes sense, because R binding to LDL, and getting taken in by the cell, etc
  • MC CwR increases when in presence of LDL - all the C voxels that also contain R
    • makes senses because means clathrin is now associating with receptor in presence of LDL - because LDL needs to be taken into the cell!
  • PC increases in presence of LDL
    • makes sense because receptor and clathrin more stoichiometrically associated when LDL needs to be taken in


AKU tissue physiology

Submitted by msgordon on Sun, 10/22/2017 - 21:46

Previously, it was thought that only liver cells expressed HGD and thus were responsible for the Alkaptonuria phenotype as ochronotic pigment would circulate in the bloodstream before being deposited in the cartilage. This was proven not to be the case as it was shown that osteoarticular cells, including chondrocyctes, also express the HGD gene and thus contribute to the AKU phenotype. Generally HGA and its related compounds are deposited in two forms. The first is a granular form that is deposited in the cytoplasm of connective cells wherease in the second case, the compounds form an "encrustment" in colagen fibers. The latter form also tends to cause local swelling in the surround tissue. In either case, continued deposition of these products leads to warping of the surround tissue as the fibers attempt to 'bridge" around the shards of ochronotic pigment. Thus, tissues affected by ochronosis tend to be brittle which greatly impedes the original function of osseous tissue. 

Toxicology/Overdose EMT Assignment

Submitted by cberg on Sun, 10/22/2017 - 20:06

I believe it is vital to expose children to drug education at a young age. If children are made aware of the risks of using drugs recreationally before they are ever in situations of drug use, they may be more likely to resist giving into the influence. One educational experience that had a large influence on me personally was in my high school health class. Recovered drug addicts from a local spectrum home came to our class to tell us their stories about the path of their addiction and the horrible life-changing detrimental effects of the drugs. The stories were moving and emotionally impacted all the students in the class. It was eye-opening to hear about how recreational use lead to addiction so quickly and uncontrollably. In my opinion, programs such as these would offer a potential solution to the toxicological abuse epidemic.

            Another program I have heard about is schools taking their students on trips to local prisons to listen to inmates speak of their drug history. Such programs give students first-hand exposure to the legal consequences of being involved with drugs. Many inmates have lengthy or life-long sentences because of their drug involvement, and hearing them personally speak about their situations would likely deter children from making the same risky decisions. I believe that both of these types of programs would be beneficial to involve children with from a young age. In addition to starting from a young age I think it would be a good idea to make the programs a somewhat consistent part of health education. Rather than only attending such events one time, I think it would make more of an impact if it were an annual event where students listened to different speakers and different stories each time. In this manner, the consequences may become more real and relevant to the students, and the emotions and reality of the risks of drugs would stick with them for longer. 

Review for Animal Movement

Submitted by alexispena on Sun, 10/22/2017 - 17:43

Taxonomy of Movement

  • Home range is the area an animal typically move within to obtain necessary resources for reproduction and survival
    • Home range size depends on body mass and diet (i.e. large carnivores have a larger home range than a large or small herbivore) and habitat type/quality
  • Stasis is when some animals never move or move only in gamete or larval stage
    • Most animals spend large portions of their day static and some spend months or years (i.e. hibernation)
  • Station Keeping: most movements that determine the home range of an animal or are resource directed movements. Movements that keep an animal within its home range.
    • Kinesis: simple changing of movement no consistent relationship to stimulus
      • Random, aimless movement
      • i.e. Sage grass males put on elaborate displays, females are not interested
    • Taxes: directed movement where the long axis of body shows a consistent relationship with stimulus
      • A fly that is focused on a light
    • Foraging: searching movement that’s readily interrupted by encounter w/resources
      • It can be extensive
    • Commuting: round-trip regular movements within the home range
      • Vertical commuting of copepods
    • Territoriality behavior: movement made to maintain or defend a territory
      • Scent marking
    • Ranging: Exploratory movements outside of home range often to look for new habitats, “dispersal”. The movement stops when new resources/habitat are encountered.
      • Term dispersal is problematic because individuals cannot disperse 

gene therapy

Submitted by dalon on Sun, 10/22/2017 - 14:40

In gene therapy, a vector (which is usually a virus), is genetically engineered to insert itself into the gene. These are useful because they can deliver the new gene, but not infect the human with a disease (after being modified). The vectors can be given through an IV or directly into a specific tissue in the body. One type of vector is the retrovirus, which infect only dividing cells. Once the retrovirus is inside the cell, it injects its RNA, which is then converted into DNA, and then the DNA from the retrovirus integrates into the normal DNA genome. The adenovirus is also used and can target both dividing and nondividing cells; however, it does not integrate into the DNA genome so after a few weeks the effects are lost. The Adeno-Associated virus also targets non dividing and dividing cells, but they need a “helper” virus to replicate themselves inside the cell. After its DNA travels to the cell’s nucleus, it will (95% of the time) integrate into chromosome 19. The Herpes Simplex Virus target cells of the nervous system. While the virus does not integrate with the DNA, it will continue to replicate its own circular DNA as the cells divide and will not disrupt the function of other genes in the host cell. Liposome also injects its DNA into the nucleus, but is not effective and will not integrate with the host DNA. Naked DNA is also a nonviral option, but it does not integrate well with the cell in the nucleus. There is also a nonviral vector called plasmid, but they are much less effective than viruses in getting the genes into the cells, but they can carry many more genes and don’t have an immune response. Synthetic vectors (liposomes covered with viral surface proteins) are also used. The surface proteins help the virus fuse with the cell membrane so it can inject the DNA contents into the


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