Arabidopsis transcriptional repressor VAL1 triggers polycomb silencing at FLC during vernalization.

Submitted by oelbetanony on Sun, 12/10/2017 - 18:50

In this paper the authors explored the mechanism of vernalization. Vernalization is the epigenic silencing of FLC. Flowering locus C (FLC) is an important regulator of flowering time. When Arabidopsis Thaliana is exposed to the cold for a prolonged period vernalization is triggered. The Authors sought out to find out what exactly silences this FLC gene in response to prolonged cold exposure. The focus of the paper was what transcriptional factor is specifically responsible in FLC silencing. The authors first determined that PHD-PRC2 was key to the silencing of FLC they then wondered what specific transcriptional factor was responsible for silencing the gene. The authors then Identified a mutant that prevented PHD-PRC2 nucleation which prevented the silencing of the FLC gene. They identified the location of this gene which pointed them to the first pair of RY cis elements. This raised the question of what transcriptional factor was bound to these RY elements and allowed the nucleation of PHD-PRC2 and the silencing of the FLC. To answer this question the authors thought of all the transcriptional factors that could be the key factor and Identified potential key transcriptional factor VAL1 because of its high levels of expression compared to the other candidates. After genetic testing of VAL1 mutants against the wildtype the results showed that VAL1 does bind to the RY elements and also recruits ASAP complex which triggers nucleation of PHD – PRC2 and allows the silencing of the FLC.

Methodological approach to melonopsin study

Submitted by oelbetanony on Sun, 12/10/2017 - 18:49

The Methodological approach consisted of first making antibodies against the C and N terminal of the melonopsin sequence to identify cells in the retina that are.expressing melonopsin. To see where these melonopsin positive RGCs are projecting the authors used Tau-LacZ to target the melonopsin gene. Using Tau-LacZ the authors were hoping to see were melonopsin was activated and projected, and see if it was projected towards the Suprachiasmatic nucleus (SCN) where circadian function is regulated. To make sure all RGCs that are projecting to the SCN are doing so due to melonopsin the authors injected Lucifer yellow into the photosensitive RGCs that projected to the SCN and cross compared with melonopsin antibodies to see if they turned up melonopsin positive. Light was also used to see if these RGCs reacted to it.

education reflection

Submitted by oelbetanony on Sun, 12/10/2017 - 18:45


This class definitely opened my eyes to a lot of things I was never aware of. One of those things is how difficult it is to teach and help students with different learning disabilities, It really takes complete understanding of a students condition to be able to properly help him/her. one thing I realized that I haven't before is how Autism is a spectrum disorder and how it differs greatly from person to person.  


Introduction Pressure Hypothesis

Submitted by jgcahoon on Sun, 12/10/2017 - 14:45

The first part of the Introduction Pressure Hypothesis says that species that arrive more times or in larger numbers are more likely to establish. When a species is introduced to a new area in large numbers, they can establish themselves into the community easier, and would multiple at a faster rate. The other part of this hypothesis says a species that arrives from many different populations acquires a higher fitness through interbreeding or by dealing with genetic drift often. An invasive species that adapts itself to various areas (populations) would be able to spread easier when it arrives to new ones, since they are used to dealing with this type of change.

Topics in Plant Bio Notes - Flowering II

Submitted by samihaalam on Sun, 12/10/2017 - 13:59

Soybean flowering is controlled more by day length than the number of “days-to-flowering”. In other words, soybeans flower based on the length of days, instead of the “age” of the actual plants. This can be shown through the farming of soybeans. Regardless of when farmers plant their soybean crop, they will all have a relatively synchronized blooming in the autumn, suggesting that the length planted was not important to the plants.


There are two types of ways that plants can bloom: short day plants and long day plants. Short day plants bloom when the days are short, such as in the autumn and winter. This includes Morning Glories. Long day plants bloom when the days are long, such as in the summer. This includes the plant Henbane.

Photoperiodism is the ability of any organism to detect day length, not just plants. Humans and other mammals have this ability as well, as evidenced by our circadian rhythms. So, this is a common ability of organisms. There are different ways to categorize the photoperiodic response in plants specifically. There are short day plants and long day plants as described above. The short day plants more specifically flower only in short days (which is a qualitative SDP response) or are accelerated by short days (which is a quantitative SDP response). Another example of an SDP is the plant Cocklebur, which remains vegetative if the day is 16 hours long, but flowers if the days are 15 hours long. This seems to be an example of a qualitative SDP response. The long day plants more specifically flower only in long days (which is a qualitative LDP response) or their flowering is accelerated by long days (which is a quantitative LDP response). For example, the plant Lolium temulentum rye grass flowers when the day length is greater than 14 hours. This seems to be an example of a quantitative LDP response. There are also day-neutral plants (DNP) which are plants whose flowering is insensitive to day length.  

Perfect Paragraph - SOD1 protein

Submitted by msgordon on Sun, 12/10/2017 - 12:27

The SOD1 protein itself is a homodimer and is normally localized to the intermembrane space (IMS) between the inner and outer mitochondrial membranes as well as the cytosol. Structurally, the protein is comprised of two β-barrel subunits that each contain bonding sites for copper and zinc ions (Sea et al. 2014). When it is first trafficked into the mitochondria the protein takes on an immature form, lacking the metal ions necessary to carry out its function. After binding, it remains in the intermembrane space with aid from the copper chaperone protein CCS. The enzyme then uses the aforementioned ions to catalyze the conversion of otherwise toxic superoxide radicals into water and hydrogen peroxide - the latter of which is broken down further by catalase (Estacio et al. 2015). One proposed mechanism involves the SOD1 protein using the copper cation to extract the extra electron from the superoxide radical, effectively converting it into molecular oxygen. Similarly, the presence of the cations are crucial to its function as the positive charges aide in attracting the negatively charged superoxide anions.

ALS - COPII protein

Submitted by msgordon on Sun, 12/10/2017 - 12:19

Deeper analysis of the role of the golgi complex indeed suggests that it plays a crucial part in the FALS mechanism. Coatomer coat protein II (CopII) is a protein essential to trafficking proteins out of the endoplasmic reticulum and into the golgi apparatus. It is important to note that upregulating CopII levels in neurons expressing mSOD1 reduces ER-Golgi trafficking and prevents neural apoptosis as a result. This suggests that the mutated SOD1 protein inhibits CopII from facilitating proper ER-Golgi protein trafficking. Furthermore, immunoprecipitation studies revealed that the mutant SOD1 proteins inhibit ER-Golgi trafficking via binding to the Sec23 subunit of CopII both in vitro and in vivo (Atkin et al. 2013).


SEP3 control in Floral Development

Submitted by rhallice on Sun, 12/10/2017 - 11:48

The MADS-box family of transcription factors are involved in all the major aspects of floral development. In different combinations, the transcription factors of the MADS-box family control the identities of the different type of floral organs of sepal’s, petals, stamens, and carpels. A study done by scientist (Kaufmann et al, 2009) preformed the first gemone-wide analysis of the binding sites of a MADS-box transcription factor in plants known as SEPALLATA3 or SEP3 using a new technique called ChIP-Seq. This new technology works by using a chemical agent in order to stabilize DNA-protein interactions in a nucleolus where then an antibody specific to the transcription factor you want is used to extract the transcription factor and the DNA that is bound to it. The DNA that was bound to the transcription factor is released and with the help of next-gen sequencing libraries of the genes are made and mapped and this helps scientist see where transcription factors bind to on the DNA. With this new technique the researchers in the Kaufmann et al, 2009 experiment found that SEP3 binds to thousands of regions within the genome of an Arabidopsis plant. This means that SEP3 must act a global regulator of gene expression during the many stages of floral development. Also sep1,2,3 mutants lacked petals, stamens, and carpels which is another example of the importance of SEP3. SEP3 has been also shown to dimerize (macromolecular complex formed by two macromolecules) with many other MADS-domain proteins. Scientists were also able to figure out with ChIP-SEQ enrichment peaks that MADS-domain protein complexes bound to two CArG box DNA sequences at short distances from one another. This was important because this finding supports the floral quartet model. The floral quartet model is responsible for floral organ identity through tetrameric protein complexes that are comprised of MADS-domain proteins. These quartets act like transcription factors that when they bind to their target genes on the DNA, they either activate or repress expression. SEP3 is the “glue” in these floral quartets due to the fact SEP3 is expressed throughout floral development and that transforming leaves into floral organs requires SEP3. SEP3 transcription factors are the regulators of flower development because of their ability to form different dimer complexes and their interaction other floral homeotic proteins being able to bind to homeotic gene promoters. This study by researchers in the Kaufmann et al, 2009 paper shows that SEPALLATA3 transcription factors are the key components in the regulatory transcriptional network responsible for the formation of floral organs in Arabidopsis plants.

Topics in Plant Bio Notes - Flowering

Submitted by samihaalam on Sat, 12/09/2017 - 15:16

Flowering in plants needs to be a very strictly temporally regulated process. Flowering is officially when the plant moves from a vegetative state to a reproductive state. It needs to occur when the plant is large enough to "feed" the seed with photosynthates. There are several environmental conditions that need to be considered by flowers before they bloom. These include temperature, moisture, light, mate, and pollinator conditions. Plants at different latitudes thus experience  different day lengths. This, of course, has an effect on the cycles within the plants that occur at these different lattitudes. Day length changes because the Earth  is tilted and revolves around the Sun at this tilted angle. Therefore, a certain lattitude will get a certain amount of sunlight during one part of the year, but a few months later, the earth has rotated around the Sun and is at a tilt, and so it will get a different amount of the sunlight. 

Plants can be categorized by their photoperiodic responses. In 1906, a mutant tobacco plant was discovered that flowers in the winter and ust grows and grows in the summer, as opposed to flowering in the summer like normal tobacco plants. This mutant plant is called the Maryland Mammoth. It's unusual flowering ability is due to a recessive gene that is involved in short-day behavior in flowers. 


Topics in Plant Bio Notes - Light Perception II

Submitted by samihaalam on Sat, 12/09/2017 - 02:00

A phytochrome has two identical proteins that join together. Each of these proteins has two domains. One of these domains is the part that acts a photoreceptor. The structure that is specifically the photoreceptor is the chromophore, which captures light and undergoes conformational change. The other domain is the kinase domain, which triggers cellular responses. The phytochromes interconvert between an inactive and an active form. The Pr form abosorbs red light, and is synthesized in this form. This is the stable form of the protein. The Pfr form absorbs far-red light and is the active state of this protein. It is also the unstable protein and is degraded quickly, indicating that the active protein is fast-acting, with short effects in the plant cells. These responses include seed germination, control of flowering, and other various responses. After the Pfr form relays it effects, it is either slowly converted back to the Pr form in darkness in some plants, or it is sent to the lysosome to be destroyed. The red light being absorbed in the plant by the chromophore results in the the cis (Pr) isomer converting to the trans (Pfr) isomer. The response to light is transfered along the cell due to the movement of the phytochrome from the cytosol to the nucleus. When in the nucleus, phytochromes interact with to regulators of transcription. Therefore, light causes changes in gene expression. Phytochromes are not restricted to higher plants. The chromophore-binding region and signaling domain are highly conserved regions in prokaryotes, bacteria, and higher plants. Phytochromes are encoded by a multigene family, that has different functions in plant cells. They are responsive to different wavelengths and light intensities. PhyA activates a response to far-red light, while PhyB activates a response to red or white light. 


Subscribe to Writing in Biology RSS