You are here

rhallice's blog

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.

Antibiotic-resistant genes

Submitted by rhallice on Mon, 12/04/2017 - 12:34

Antibiotics play an important role in modern medicine as prophylactic treatment for cancer therapy and during surgeries. However the rise of resistance of bacteria to these antibiotics are causing problems posing a real danger in places like hospitals. Antibiotic resistance genes can spread in many different ways. One way is through plasmids that have these resistant genes encoded on them. However thanks to the hard work of scientist at the University of Montreal’s Department of Biochemistry and Molecular Medicine, a new approach to block this transfer of the resistant genes was developed. They screened a library of small chemical molecules for those that would bind to protein TraE, a component of the plasmid transfer machinery. Now that more information about the binding site is known, researchers can design more potent binding molecules that will in turn reduce the key transfer of resistant-antibiotic genes through the plasmids. One of the Scientist Christian Baron hopes that in the future with further research that this strategy can be used to discover more inhibitors of the transfer of resistant genes. University of Montreal researchers and chemists are now working on developing new molecules into powerful inhibitors of resistant gene transfer and hopefully these molecules can be applied in clinics in hospitals. 


Submitted by rhallice on Thu, 11/30/2017 - 20:31


This Article discusses Noroviruses and how they are the number one cause of food-borne gastroenteritis and childhood diarrhea. Noroviruses are transmitted by contaminated food/water or through direct person to person contact. Noroviruses are single-stranded positive-sense RNA that are non-enveloped with an icosahedral shape. Not much was known about this viruses let alone what they targeted within the body, These scientist sought to find the targets of this norovirus in order to further understand and better treat this infection. What the researchers found was sure stunning. They had found that the major targets of these noroviruses were the Immune Cells that were heavily associated with gut-associated lymphoid tissue like macrophages, dendritic cells, B cells, and C cells. The lymphatic system is the bodies defense mechanism against harmful pathogen and lymphoid tissue are the cites in the body where the ever important lymph immune cells are produced..


Submitted by rhallice on Thu, 11/23/2017 - 22:19

The famous Englishman Alan Turin played a crucial role in decoding messages by the German Enigma machine during the Second World War, helping allied forces win the war. In 1952 he published the famous book on mathematical biology called The Chemical Bases of Morphogenesis developing his Turing-type reaction-diffusion system. For years scientist had believed that digit formation was controlled by a morphogen gradient of Sonic Hedgehog (Shh). A morphogen gradient is a developmental biological concept where the emission of a signal from a part of an embryo can determine the location, differentiation, and fate of the surrounding cells through the morphogen’s concentration. It was thought that the Shh morphogen controlled digit formation and that GLI3 transcription factor controlled the expression of Shh. However, researchers found the GLI3 and Shh mutants had displayed identical phenotypes of polydactyl limbs, or hands with more fingers. This in turn shows that digits can form in the absence of Shh. This is not a consistent observation that would support a morphogen gradient model. This shows that digits can form independent of Shh meaning that Shh gradient can pattern digit identity but is not a factor in determining where a digit occurs. However, this supports a Turing-type model in digit pattern where an interaction of activators and inhibitors plays a role in the wavelength and patterning of digits. A Turing-type reaction-diffusion mechanism involves an activator that also turns on its on inhibitor as well where the activator diffuses in a short distance and the inhibitor can diffuse further producing a repeating pattern. This repeating pattern resembles a wavelength of peaks over a distance.

Hox Genes and Wavelengths

Submitted by rhallice on Thu, 11/23/2017 - 22:18

Hox genes are a group of related genes that control the body plan of embryos and Hox proteins determine appendages. Distal Hox genes Hoxa13 and Hoxd11-Hoxd13 were found to be the Hox genes involved in digit formation. GLI3 is the mediator that modulates the expression of distal Hox and acts as their inhibitors. Hox gene mutations caused more digits formed that were thinner and closer together. Some more extreme mutations caused all mutations to connect to one another forming almost a paddle looking hand. Also shown was that the hand size itself did not increase but only the number of digits changed. There is a correlation between distal Hox gene number or dosage level and digit wavelength in a model of a Turing-type reaction-diffusion mechanism. The lower the expression of Hox genes by mutants caused the increased digits of phenotypes and that is why if there was an over expression of these distal Hox genes then we would see less but much thicker digits. 

PefectParagraph Nov6-10

Submitted by rhallice on Fri, 11/10/2017 - 11:28


In plants, there stem cells are located in the shoot meristem where WUSCHEL (WUS) homeobox genes and CLAVATA 3 (CLV3) genes are constantly being expressed through negative feedback loops. When plants want to grow, the shoot meristem WUS, a transcription factor, specifies stem cell identity for growth when it is expressed. WUS also turns on its own repressor CLV3 as well that in turn regulates shoot meristem size. This negative feedback loop is important in plant growth and regulation. CLV3 is a signal peptide that binds to CLV1 a receptor complex however the exact pathway for modifying CLV3 and its applicability for CLV signaling are unknown.

Morphogen Concentration

Submitted by rhallice on Sun, 11/05/2017 - 14:38


            Morphogens are chemical agents that are typically produced by source cells and diffuse across the surrounding tissues of an embryo setting up a concentration gradient. This concentration gradient of a biomedical molecule determines the fate of embryo development and also supply the positional information to cells in an embryo.  Drosophila also known as fruit flies make for the perfect model organism for studying embryonic development and genetics due to their numbers and ease of access. In a recent study scientist found that dorsal, a maternal effect gene, encodes for a morphogen gradient that regulates the development of ventral embryo structures. Drosophila embryos are separated into two major and important axes patterning: the anterior-posterior axis and the dorsal-ventral axis. The dorsal-ventral patterning axis determines the back (dorsal) and front (ventral) side of the embryo and is dependent on the ventral nuclear concentration of dorsal. The dorsal side of the embryo is developed when oocyte nucleus moves from posterior to anterior side of the embryo and expresses a protein called Gurken. When Gurken is present it repress the production of Pipe protein. The pipe protein is important in the pathway to get dorsal a morphogen into ventral nuclei and therefore to determine ventral identity. However once expressed Pipe begins the extracellular cascade to turn on Toll receptors on ventral embryo cells. This cascade continues intracellularly to separate the dorsal morphogen from Cactus. Once separated form Cactus, dorsal is able to move into the nucleolus of the ventral cell to act as a morphogen. Once inside the nucleus, the dorsal activates different genes depending on its concentration setting up a gradient turning on transcription factors twist and zen which in turn results in the formation of the embryonic mesoderm. The mesoderm (middle layer) is one of the three germ layers that are developed in an early embryo and arise to form muscle tissues and red blood cells.


CLAVATA Perfect Paragraph

Submitted by rhallice on Thu, 10/26/2017 - 18:34

The Researchers used mutants with larger stems and tomato fruits to find out what caused these mutants, more specifically how the CLAVATA signaling pathway is regulated. The researchers used forward genetics, an approach that is used to identify genes. They used a technique called CRISPR/Cas9 and found that arabinosyltransferase genes were essential for the control of meristem size and plays a major role in the CLV pathway. They used mutants and there phenotypes to support this hypothesis. They found that fab and fin mutants in tomatoes had larger meristems than normal wild types. After discovering these mutants researchers cloned the genome regions of the DNA that caused the fab and fin mutants. They mapped these mutants and found that fab codes for CLV1, the receptor in the pathways while fin codes for arabinosyltransferase, what seems to be the unknown link in this pathway that the scientists sought to find. In the fin mutants the researchers also found that SICLV3 a signal peptide was being expressed at a higher rate. The scientist think that fin adds a arabinose onto SICLV3 and they used this to rescue the fin mutants meaning that the SICLV3 with arabinose had tomatoes of normal sizes. The work of these researchers using forward genetics, mutations and rescuing phenotypes they found the CLV3 with FIN wild type and the arabinosyltransferase enzymes of FAB2 and SIRRA3a were used to activate the FAB receptor. Remember that mutant fab caused much larger meristems. This, the researchers discovered was the missing pathway that scientists were looking for.

PP #6

Submitted by rhallice on Thu, 10/19/2017 - 20:00

This experiment and findings is a very important turning point when healing and treating diabetic patients with wounds that easily get infected from microorganisms causing damage. Modern medicine is always evolving every day so it is very important to stay up to date with all the growing advancements to improve health care and improving the well-being of patients.  

PP #5

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

This journal discusses the treatment of diabetic wounds and how to heal them and protect these wounds form microbial infection. Historically the treatment of Diabetic wounds requires a very large amount of growth factors so the researchers developed a strategy using a payload comprising of Eudragit RL/RS 100 nanofibers carrying gentamicin sulphate (GS) a bacterial inhibitor in a concentrate with the human epidermal growthfactor (rhEGF), a wound healing accelerator. This is important because diabetes is a barrier to proper wound healing that can lead to infection or worst case amputation. They used scanning electron microscopy, fourier transform infrared, spectroscopy and X-ray diffraction in order to characterize this new fabricated nanoscaffold. The subsequent research that followed this experiment showed much improvement to healing wounds then traditional bandages.



Subscribe to RSS - rhallice's blog