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Topics in Plant Bio Notes

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

Bryophytes:

  • large gametophytes, small sporophytes 

Vocab:

Sporophyte:

  • sporangia = where meiosis produces spores

Gametophyte:

  • 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

changes:

  • 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

 

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

A:

  • 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

 

Comm 118 Study Guide Exam 2

Submitted by samihaalam on Fri, 10/20/2017 - 21:58

1. Comm as:

  • primary social process
    • persons in conversation
    • look at what people do in conversations to understand people, religion, politics, ethniticities, etc
  • formative
    • of meanings
    • of selves in socieities
  • face-to-face
    • prototype of communication - all other forms of comm compared to this, based off this
    • counter to idea that electronic texts are more important
  • interactive
    • dialogic 
  • meaningful
    • counter to idea of simple transmission of ideas
  • cultural
    • particular expressive system 
    • counter to idea that comm is the same, everywhere

2. Meaning-making

  • role of terms, phrases
    • used as symbols
  • forms-sequences
    • sqeuences of actions
  • terms and forms = premises of meanings
  • Brad Hall!
    • on a bus: "escuse me, would you mind moving over so I can sit?" vs. "move over."
  • Blackfeet people!
    • Northern Montana
    • old and young speak the language
    • not just about how much Blackfeet "blood" you have - also about how you act, the traditions

Cell and Molec Notes 10/17

Submitted by samihaalam on Fri, 10/20/2017 - 19:16

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

A:

  • 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?
  • → 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 stuf contains LDL; different things!

Legend for Sabaody_Archipelago Data

Submitted by samihaalam on Fri, 10/20/2017 - 15:11

Figure 1: Graphical Analysis of Data from Sabaody Archipelago 

This figure is a graphical analysis of the data from sabaody archipelago to visualize correlations between GPA, hours slept per week, hours studied  per week, and gender. The most relevent trends in the graphs are visualized in the hours slept versus GPA and hours studied versus GPA. In the hours slept versus GPA graph both males and females had a positive correlation between hours slept and their GPA. In the hours studied versus GPA graph, females had a positive correlation between the hours studied and their GPA. Men did not exhibit a correlation. The outliers in the data set with an O for gender, 100 hours for hours studied per week, and 5 hours for hours slept per week were removed to make more concise graphs. 

Planarian Project Start

Submitted by samihaalam on Thu, 10/19/2017 - 23:54

Planarians have been observed to have an aversion to light, and thus spend more time in darkness than in light. In one study, researchers created a new method to study this phenomenon. These researchers filled a Petri dish with water or a different compound and put a planarian in the middle. They had the dish split into even amount of light and dark portions, and recorded for 10 minutes the amount of time the planarian spent in either compartment. I think this could be a reasonable and simple experiment to recreate in this class. 

Methods Project Goals

Submitted by samihaalam on Sun, 10/15/2017 - 22:29

There are multiple goals in this project. The primary goal is to create a multi-panel figure that to be described and replicablated by another classmate. From this, we should also gain an appreciation for designing an experiment that is easily replicable. Another aim is to be able to appreciate and identify all the necessary controls that one must consider when designing an experiment. A more long-term goal is to be able to distinguish between an observation and an inference. This project should teach us a variety of skills to help us become better scientists.

 

Methods Project Discussion Re-Write Part II

Submitted by samihaalam on Thu, 10/12/2017 - 19:59

Different things can be seen in panel A in Figures 1 and 2 probably because the orientation and height of the camera were probably different from they were in the original photo. Although these were specified in the Methods, approximate heights/distances were given, which may have led to these differing results. The leaves in B, C, and D all had different patterns of variegation between Figure 1 and their corresponding panel in Figure 2. This can be explained because different leaves were probably used in Figures 1 and 2. This is probably because the Methods did not specify clearly enough where the exact leaves that were used in the original photos were located. 

 The fact that in panel B in Figure 1, the ruler uses cm, but in panel B in Figure 2, the ruler uses mm allows me to infer that different rulers were probably used in generating these two flowers. The arrow heads and lengths were different most likely due to the fact that these specific characteristics were not specified clearly enough in the Methods section. The pictures taken in C and D show more of the background leaves in Figure 2 than they do in Figure 1 could be due to a variety of reasons. Perhaps the camera was held further away from the leaves in Figure 2 than in Figure 1, or perhaps the cameras' default settings were different. It is also possible that the different types of iphones were used entirely. 

Anoter factor that contributed to differences was the weather. The weather was almost certainly different from when the replicate photo was taken than from when the original photo was taken. Although the weather was specified in the methods, this factor could not be controlled by the person doing the replicate photo. Thus, the sunlight and brightness in all the panels differ slightly between the two figures. 

A different type of iphone may have been used to take the photos. This may be an explanation for why the overall size of the images are different. The original photos may have been uploaded, and then scaled accordingly, but if the original photos' were different sizes, then when they were scaled, they would have been different sizes. This would have led to a difference in sizes overall between the two figures. This may also be a reason as to why the photos appear to be scaled differently. 

Methods Project Discussion Re-Write

Submitted by samihaalam on Thu, 10/12/2017 - 14:23

Different things can be seen in panel A in Figures 1 and 2 probably because the orientation of the camera  and the position in wich the person stood were different. The leaves in B, C, and D all had different patterns of variegation between Figure 1 and their corresponding panel in Figure 2. This is can be explained because different leaves were probably for Figures 1 and 2. The fact that in panel B in Figure 1, the ruler uses cm, but in panel B in FIgure 2, the ruler uses mm allows me to infer that different rulers were probably used in generating these two flowers. The arrow heads and lengths were different most likely due to the fact that these specific characteristics were not specified clearly enough in the Methods section. The pictures taken in C and D show more of the background leaves in FIgure 2 than they do in FIgure 1 could be due to a variety of reasons. Perhaps the camera was held further away from the leaves in Figure 2 than in FIgure 1, or perhaps the cameras' default settings were different. It is also possible that the different types of iphones were used entirely. 

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