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Limb devo 2

Submitted by daniellam on Mon, 11/20/2017 - 21:52

Hox is a turing model not a gradient model like Shh

Hox uses the turing model which forms alternating and repeating patterns using an activator and an inhibitor. The activator turns on itself and the inhibitor that is far away from the activator. Once the inhibitor is on, it turns off the activator as well as itself. These two interact to form a standing wave, showing areas where the activator is on (inhibitor off) and others where the inhibitor is on (activator off) (Bartlett 2017).

Digits form independently from Shh

Scientists found that the formation of fingers used the Turing model rather than the gradient model by removing Shh and Gli3 which both use the gradient model. What they found was that even after removing Shh and Gli3, fingers still formed. During development, Hox works by regulating this Turing model and increases the wavelength. The increase in wavelength allows for correct finger formation. Without this increase in wavelength, the spaces in between the fingers do not form properly and extra fingers can form. The scientists observed this phenomenon by removing Hox genes from developing mice embryos (Fig. 3). The hands with more Hox genes removed had more, thinner fingers with less space in between. After removing all of the Hox genes, they saw that there was only a stump (Sheth et al. 2012).

Limb devo

Submitted by daniellam on Sun, 11/19/2017 - 22:53

Scientists from Spain have discovered a way to not only increase the amount of fingers in mice but increase them to the point that they all connect to one another and form a stub for a hand. How is this possible? Fingers form from the hand during development in a wave-like fashion. If one imagines a standing wave with multiple peaks, in this case, the peaks pointing upward are the fingers and the spaces in between the peaks are the spaces in between the fingers. The spaces from the hand to the fingertips increases. This increase in space is due to a gene called Hox. Unlike its counterpart, Shh, which forms the identity of the fingers, Hox determines the number of digits formed. When there is a mutation in this gene (the gene stops working), extra fingers form on the hands (Sheth et al. 2012). 

mutagenesis discussion

Submitted by daniellam on Sat, 11/18/2017 - 00:18

The number of yeast colonies for both UV exposure times were substantially low, even lower than expected values. Of the 1000 estimated yeast colonies placed on the YED plate prior to UV exposure, 200 (20%) were supposed to survive and recover from the DNA damage, and from that recovery there were supposed to be some mutants. Due to higher levels of radiation from the transilluminator, more yeast were killed than anticipated. For future experiments, this can be resolved by reducing exposure time and increasing the yeast population on the plate before exposing them. This method relied on the chance that a mutation would be introduced into the yeast through a problem occurring with DNA repair.

The FOA plate had 7 colonies, which means that the yeast mutated in order to stay alive in that plate. They gained the inability to produce 5-fluoro-uracil which is a self toxin. Only one other group in a different lab period also had colonies in their FOA plate. This indicates that inducing this specific mutation or any specific mutation is a rare occurrence and is not guaranteed to happen.

Abstract for yeast (perf)

Submitted by daniellam on Fri, 11/17/2017 - 01:54

There are two ADE genes (ADE1 and ADE2) in yeast that must both be functional for them to produce adenine properly. When a haploid with a mutation in ADE1 mates with a haploid with a mutation in ADE2, the two functional halves of the ADE genes complement each other and form a diploid. Complementation can be useful for identifying the ADE mutation of unknown yeast strains. The simplicity of complementation in yeast exemplify a complex mechanism, in which two alleles with different functional parts can complement each other to form an important phenotype. The identification of the unknown mutants came out to be: MA1 is an ADE1 mutant, MA2 is an ADE1 and ADE2 mutant, MB2 and MB4 are ADE2 mutants. These experiments used yeast as a simple model to show the mechanisms of complementation which are complex and an important part of acquiring phenotypes.

Abstract for yeast

Submitted by daniellam on Fri, 11/17/2017 - 01:39

There are two ADE genes (ADE1 and ADE2) in yeast that must both be functional for them to produce adenine properly. When a haploid with a mutation in ADE1 fuses with a haploid with a mutation in ADE2, the two working halves complement each other and form a diploid with both working ADE genes. Complementation can be useful for identifying the ADE mutation of unknown yeast strains. The simple complementation in yeast exemplify a complex mechanism in which two alleles with different functional parts can complement each other to form an important phenotype. MA1 is an ADE1 mutant, MA2 is an ADE1 and ADE2 mutant, MB2 and MB4 are ADE2 mutants. These experiments used yeast as a simple model to show the mechanisms of complementation which are complex and an important part of acquiring phenotypes.

Part of study guide for neuro

Submitted by daniellam on Wed, 11/15/2017 - 22:58

Overall structure of the eye and the general function for those structures

  • Retina: light sensor for eyes
    • Transduces light into neural impulses
    • Portion of the CNS
    • Blind areas: optic nerve and blood vessels
    • Parts of retina
      • Photoreceptor cells: main light sensors
        • Rods (scotopic): 1000x more sensitive to light than cones
          • For dim light, outnumber cones 20:1
        • Cones (photopic): for bright light
          • Humans have RGB cones
      • Ganglion cells: only output cells
      • Bipolar cells, horizontal cells, amacrine cells
  • Cornea: light refraction (most)
    • Refractive power is reciprocal of focal distance
  • Lens: also refracts light (little)

 

Accommodation and vision correction

  • Accommodation: ciliary muscles contract to focus on closer objects
    • Relaxed: flat lens, see far points
    • Contracted: fat lens, see near points
  • Vision correction
    • Far sighted (hyperopic): can’t see close
      • Image focused behind retina
      • Correct with convex lens
    • Near sighted (myopic): can’t see far
      • Image focused before retina
      • Correct with concave lens
    • Astigmatism: need asymmetric lens

 

The signaling pathway for how photoreceptor cells transduce light

  • In the dark:
    1. Rhodopsin (pigment containing membrane receptor) is inactive
    2. G-protein is inactive
    3. Phosphodiesterase is inactive
    4. cGMP bound to Na+ channel à open
    5. Depolarized membrane potential: neurotransmitter release
  • In the light:
    1. Photon light activates rhodopsin
    2. Rhodopsin activates G-protein (replaces GDP with GTP)
    3. G-protein activates phosphodiesterase
    4. Phosphodiesterase cleaves cGMP to GMP
    5. No cGMP bound to Na+ channel à closed (due to low cGMP)
    6. Hyperpolarized membrane potential: decrease in neurotransmitter release
  • Amplification of signal due to signaling cascade
  • Lower rate of neurotransmitter release in response to light à increased 1000x due to cascade
  • Darkness activates photoreceptors
  • Phototransduction in cones: opsins mix to form color variations, perceive color during photopic vision

 

General principles of retinal processing and receptive field properties of cells throughout the visual system

  • Dark/light adaptation factors
    • Pupil size
    • Regenerate state of rhodopsin
    • Retinal circuitry: #rods/ ganglion cell
    • Calcium and guanylyl cyclase (enzyme that makes cGMP)
      • (when dark) channel is open and Ca2+ in the cell inhibits guanylyl cyclase à lower amounts of cGMP
      • Feedback loop, allows adaptation
    • Channel closed in light but gradually reopened
  • Retinal processing
    • Receptive field: area of retina that causes change in membrane potential
    • Bipolar cells have center-surround receptive fields: generated by interactions with horizontal cells
      • On center Bipolar cells
        • Light hits center: depolarize (less glutamate)
        • Glutamate: hyperpolarize (have glutamate G protein receptors) inhibitory
      • Off center Bipolar cells
        • Light hits surrounding: hyperpolarize (less glutamate)
        • Glutamate: depolarize (have glutamate ligand gated ion channels) excitatory
    • Bipolar receptive field transferred to ganglion cells
      • Action potentials
      • On-center and off-center fields
      • Off center ganglion cells fire more AP when the surrounding is lit
    • Importance:
      • Generates neural response for contrast between light and dark edges
    • Different types of RGCs (differ in size and firing properties) that project to different layers of LGN and remained separate
      • Magnocellular (5%)
      • Parvocellular (90%)
      • nonM-nonP (5%)

Results for distillation

Submitted by daniellam on Tue, 11/14/2017 - 23:37

Plateaus in temperature are sought out for good distillation because it means that the liquid and vapor of the mixtures are at equilibrium. This is important for distillation because it creates a condition called total reflux which creates a good separation (Zubrick 179).  In the second temperature profile, there are many plateaus suggesting that the separation of the two compounds are at equilibrium and is much more effective.  There are drops in temperature at certain points which is a sign of a successful separation. At the first drop in temperature, it shows that there is no more vapor meaning that at this point, there would a low amount of cyclohexane left. The second drop in temperature, which occurs at a volume of 32 mL, shows the cyclohexane running to completion.  The final plateau of this temperature profile indicates that there is only toluene with a corresponding ratio of approximately 99:1 of cyclohexane.

Part of analysis for gas chromatography

Submitted by daniellam on Tue, 11/14/2017 - 11:20

Based on the gas chromatography/mass spectroscopy data, it is seen that the experiment with the simple distillation of the first sample (2nd fraction) shows a higher percent area for toluene (36.74%) compared to the fractional distillation of toluene (25.62%), suggesting that the fractional distillation went much better. This means that during the distillation, not only cyclohexane was distilled, but also some toluene.  For fractional distillation, the packing allowed a higher ratio of cyclohexane to vaporize while both of them condensed onto the copper column.  This creates better separation between the two compounds.  Similarly, for the second sample (2nd to last fraction) that was taken for simple distillation, the GC/MS shows that there is very little cyclohexane (6.14%) while the majority is toluene (93.86%).  However, fractional distillation had a much better separation since the remainder of cyclohexane (1.49%) is miniscule to toluene (98.51%).  Though most of the cyclohexane was separated from the toluene, the two compounds could not be completely separated from both simple and fractional distillation.  Fractional distillation is better for separation than simple distillation because of this packing.

simple and fractional distillation conclusion

Submitted by daniellam on Tue, 11/14/2017 - 00:56

A mixture of cyclohexane and toluene were separated using both simple and fractional distillation.  The fractional distillation showed a much better separation than simple distillation, both proven in the temperature profiles and in the GC/MS taken.  The packing of copper in the columns influenced the separation the most and is the main distinction that makes fractional more successful than simple distillation.  To have better separation in the future, a longer column could be used as well as compounds with a larger boiling point difference.  Specifically for fractional distillation, a column that is packed with more copper can increase chances of complete separation.

MV plate yeast mutants

Submitted by daniellam on Sun, 11/12/2017 - 15:54

The MV plate for Identifying mutant strains showed how complementation can allow for the identification of unknown mutant strains. For MA1, the parental strain turned pink in the MV media, this indicated that it may be an Ade1 mutant since it takes time for metabolize CAIR; but this gave time for white coloration to form before the red coloration set in (turning the color pink). The MA1/HB2 mating turned white showing complementation; since HB2 is an Ade2 mutant, MA1 must be an Ade1 mutant to complement. The MA2 parental strain turned pink, this may mean that MA2 also has a mutation in the Ade1 gene. All of the MA2 matings were either red or pink, indicating that MA2 may be a mutant for both Ade1 and Ade2; there is no complementation that occurred. Another possibility is that the MA2 strain is a mixture of multiple strains of yeast since other groups in the laboratory received positive results for complementation with MA2. The MB2 parental turned red meaning that it may have a mutation in Ade2. The MB2/HA1 mating further supports MB2 being an Ade2 mutant because it turned white, meaning that there was complementation between HA1(Ade1 mutant) and MB2 which must be an Ade2 mutant. A similar pattern can be seen with MB4: the parental is red and the MB4/HA1 mating turned white. This means that MB4 is also an Ade2 mutant (Table 2). 

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