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in class persuation argumnet

Submitted by jdantonio on Fri, 03/24/2017 - 15:06

If only one breed of dog could be saved from this retrovirus then our group (group 5) proposes that we save the alaskan malamute. The alaskan malamute is among the oldest breeds of dogs being among the 16 basal dog breeds and thus has the potential to allow for the recovery of modern breeds from the more ancient lineages. The alaskan malamute is also very hardy being bred for endurance and stamina.  They are trainable dogs that are capable of being used as sled dogs. Malamutes are highly affectionate towards humans being protective and make great family pets.

epigenetic pp

Submitted by jdantonio on Fri, 03/24/2017 - 10:32

Epigenetic modification is associated with the inheritance of many different genetic disorders, two of which are angelman syndrome (AS) and prader willi syndrome (PWS). Two closely related genes that are associated with maternal and paternal line genetic imprinting, a type of epigenetic modification, and de novo deletions cause these disorders. In PWS the gene that creates the functional gene product is imprinted in the maternally inherited mammalian chromosome, this is usually compensated for by the presence of the functional gene in the paternal chromosome. PWS is caused by a de novo deletion of the paternal copy of the PWS gene, coupled with its maternal imprinting this causes the individual who inherits these chromosomes to have no active functional copy of the PWS gene and thus causes PWS. The AS gene is conversely imprinted in the paternal chromosome of mammals and is compensated for by the expression of the AS gene in the maternal chromosome. In AS the AS gene has been lost on the maternal chromosome by a de novo deletion of the AS gene. With the paternal copy of AS inactive do to imprinting and the maternal copy of AS lost to deletion, no functional copy of AS is present and the AS disease phenotype occurs. These genes are said to be sister diseases as their inheritance is mirrored, one caused by paternal imprinting and maternal deletion the other by maternal imprinting and paternal deletion, and they are located in the same region of the chromosome. Together AS and PWS provide an excellent example of epigenetic effects on trait inheritance. 

Epigenetic diseases

Submitted by jdantonio on Fri, 03/24/2017 - 01:32

Epigenetics is the study of gene expression modification that does not change the genetic sequence of a DNA segment. There are a number of different mechanism by which epigenetic modification occurs, the first discovered of which is DNA methylation. DNA methylation occurs when a methyl group is added to the DNA molecule this in turn cause the condensation of chromosomes from euchromatin which can be read to heterochromatin which is to densely packed for gene expression. This chromosome condensation thusly prevents gene expression even though the gene itself is present in the nucleus, such a gene is said to be silenced.

 Epigenetic modification is associated with the inheritance of many different genetic disorders two of which are angelman syndrome (AS) and prader willi syndrome(PWS) which are two closely related genes that are associated with maternal and paternal line genetic imprinting( another term for DNA methylation).  In PWS the gene which creates the functional gene product is imprinted in the maternally inherited mammalian chromosome, this is usually compensated for by its presence in the paternal chromosome. PWS is caused by a de novo deletion of the paternal copy of the PWS gene, coupled with its maternal imprinting  this causes the individual who inherits these chromosomes to have no active functional copy of the PWS gene  and causes PWS. AS is conversely imprinted in the paternal chromosome of mammals and is compensated for ny the expression of the AS gene in the maternal chromosome. In AS the AS gene has been lost on the maternal chromosome by the de novo deletion of the AS gene. With the paternal copy of AS inactive do to imprinting  and the maternal copy of AS lost to deletion no functional copy of AS is present and the AS disease phenotype occurs. These genes are said to be  sister diseases as their inheritance is mirrored, one caused by paternal imprinting and maternal deletion the other by maternal imprinting and paternal deletion, and they are located in the same region of the chromosome.  

 

Holliday R. 2006. Epigenetics a Historical Overview. Epigenetics 1(2): 76-80. Taylor and Francis.< http://www.tandfonline.com/doi/pdf/10.4161/epi.1.2.2762>. Accessed 2017 Mar 24.

Nicholls RD and Knepper JL. 2001. Genomic organization, function, and imprinting in prader willi and angelman syndromes. Annual Review of Genomics and Human Genetics 2: 153-175. Annual reviews. <  http://annualreviews.org/doi/full/10.1146/annurev.genom.2.1.153>. Accessed 2017 mar 24.   

observations of a gecko

Submitted by jdantonio on Fri, 03/24/2017 - 00:30

The organism is approximately 5 inches long and has four limbs and a tail. The organisms tail takes up approximately one third of its body length. The organism has a color pattern of mostly mustard yellow scales covering  its sides and underbelly with patchy white scales along its back. And tail. There are seven patches of white scales on the organisms back but they are not wholly white as some scales in the pache are the same yellow as the belly and sides giving the patches a patchy look as well. The last cm of the organisms tail is the same mustard yellow as his belly. He has eyes that are the same shade of yellow as his side and bottom scales and he has black slit like pupils that run the entire length of his eye ball.  The organism has five fingers with claws on his front legs and right rear  feet but only has 4 on his left rear foot. The orgaims has a set of tiny spines a few mm tall that run the leg of his back in parallel framing the outside of the top of his back and head.

The organism also has two nostrils on the front of his snout. The organism tends to seek the highest point possible when in environment, climbing to the top of the tree branch in its terrarium or to the shoulder of a person handling it. When asleeep the orgaisms constrics its body into a tight ball. This may be to conserve body heat as it is a reptile and therefore lacks warm blood to maintain body temperature. The organism has a tendency to lay in the warmth of the terrariums heat lamp. The organism has the ability to jump over a foot. The organism displays an eyeball licking behavior possibly to clean the eye. The organism tends to grip objects he climbs on with both his hands and arms wrapping both legs and arms around object he climbs on.

cancer genetics project 2 Introduction rough draft

Submitted by jdantonio on Thu, 03/23/2017 - 23:34

Prostate cancer is among the most diagnosed cancer types in men ranking in the top ten in terms of cancer diagnoses and number three in deaths related to cancer among men. While a majority of prostate cancer does not metastasise the forms of the cancer that do are among the most aggressive of all metastatic cancers. Prostate cancer is rare in younger men but is common among older men by age 65 about six in every ten men are diagnosed with prostate cancer. There significant study into the effects of the environment on prostate cancer prevention, among them is diet where it has been found that isoflavone and lycopene rich foods such as tomatoes and soybeans can help to significantly reduce the chances of developing prostate cancer. The metastatic form of prostate cancer is extremely aggressive and invades multiple body tissues but its most common site of metastatic secondary tumor formation is the bones and the lymph nodes. The metastatic form of prostate cancer invades the tissues of other organs by first developing a pre metastatic niche in the area of future tumor colonization. The release of HIF-1 stimulates the upregulation of CXCR4 in the osteocytes of the human body. This upregulation in turn causes a number of changes to the non cancerous cells to modify the area for tumor colonization. For this project we will be targeting the the pathway activated by CXCR4 that activates the extracellular remodeling protein MMP-9 which remodels the extracellular proteins of  bone cells to make cancer stem cell adhesion easier and thus allows cancer cells to congregate in the bones and form a secondary tumor. In conjunction with this we will target the cancer stem cells themselves by down regulating wave-3 and scr genes which are associated with cell motility allowing the class to leave the primary tumor and cells adhesion allowing the cells to bind to no cancer niches in the bones and lymph nodes. This in combination with the modifications to the to the MMP-9 pathway in the pre metastatic niche will stop cells from migrating form the tumor and prevent any cells that do manage to leave the tumor form coming together to form a secondary tumor.

cancer genetics check in part 2

Submitted by jdantonio on Thu, 03/23/2017 - 22:27

For cell adhesion and motility we plan on also targeting the wave-3 and scr pathway which would decrease cell extracellular matrix remodeling in the primary tumor cells. Wave-3 dictates the remodeling of cellular matrix in the primary tumor allowing cancer cells to detach and leave the tumor while scr control gene the ability of cells once in the blood to adhere to the pre metastatic niche. In combination with our treatment of the niche this would prevent tumor spread to new areas by preventing the cells from leaving the primary tumor and making it hard for them to adhere to cells if they make it out of the tumor. The down regulation of miRNAs that are responsible for up regulation of remodeling genes could be accomplished by the use of microRNA sponges sequences of repeated 25 bp repeated sequences that complement the miRNA strands. This would cause the miRNA to bind to the sponge sequence and thus make them unable to bind their target sequences  For angiogenesis I plan to work with jill and develop an anti angiogenic treatment to further prevent the spread and survival of secondary tumors. Also with cell signalling we’re looking for a way to target prostate cancers very large oncosomes (exosomes) and thus disrupt communication from the primary tumor to the secondary tumor sites such as the lymph nodes. The large size of the exosomes present a rare opportunity to remove many pro metastatic agents from the blood at one time. We will further this reduction in angiogenesis through  cryo treatment the localized freeing of lymphatic and vascular tissue created by the cancer cells. Through a series of biomarkers it is possible to identify and isolate the cancer vasculature and lymph only and thus allow us to target only diseased tissues

cancer genetics project 2 check in part 1

Submitted by jdantonio on Thu, 03/23/2017 - 01:02

For our project we are choosing to target prostate metastatic cancer, it is the 6th most commonly diagnosed cancer in men and is the most deadly. Prostate cancer has a tendency to colonize bone cells and lymph nodes for secondary tumor formation. We will target the growth and proliferation of new cells with androgen deprivation therapy, which blocks the binding of testosterone to prostate cells thereby preventing prostate cell growth and survival. We will address the invasion of bone cells with Bisphosphonates and Denosumab both of which prevent the spread of cancer to the bones by interfering with bone structural features wih make it easier for cancer cells to colonizes them. we will be targeting the overexpressed receptor molecule CXCR4  which is associated with the formation of premetastatic niche in osteocytes in prostate cancer patients. We are investigating the possibility of CXCR4 down regulation by targeting miR 218 a microRNA associated with CXCR4 upregulation and miR 25 which is associated with down regulation or designing our own siRNA that specifically targets the CXCR4 gene. CXCR4 receptor activates a pathway that activates the expression of MMP9 an enzyme which remodels the extracellular matrix of bone cells. This remodeling of extracellular matrix is associated with secondary  metastatic tumor formation in the bones of metastatic prostate cancer patients. We may also target the MMP9 protein itself by designing an inhibitor for the enzyme. This covers both the premetestatic niche and extracellular matrix portion of the project.  For targeting the signalling from the tumor to new sites we plan on targeting large oncosomes, very large exosomes that are associated with prostate cancer, I have yet to find a way to target them but they’re huge so we might just be able to filter them out of the blood in a dialysis type treatment( this is little convoluted but it would be cool if it worked).

observations of a floral arrangement

Submitted by jdantonio on Fri, 03/17/2017 - 12:09

The floral arrangement has what appear to be multiple species of plant.  All the plants have their stems submerged in a vase filled with water. There are 7 types of flowers visible in the vase. One flower is a larger single flower on a single stem that has elongated yellow petals and a yellow and central area containing the pistil and stamen. Another is a single flower per stem and has wide ruffle like petals that are a mosaic of white and purple. The third type of flower has white petals that are intricately interlocked in a tight flower that appears to be a rose type of flower.   Another type of flower is a cluster of flowers per stem consisting of small green yellow flowers dark brown central regions. Additionally there is a plant with multiple flower buds that appear to not have fully developed or has some kind of spherical flower which is colored purple. Finally there is a flowering plant which has a cluster of of moderately sized flowers that consist of four larger white leaf shaped petals around a smaller white bud in the center.

There are also three species of non flowering plants in the vase which appear to only have leaves. One flowerless stem has elongated leaves approximately 4 inches long and 1 inch wide that are surfboard shaped and have a waxy looking bright green top and a dull green underside. The elongated leaf plant also has three distinct lines running down the center, right and left of the plants leaves. The second non-flowering plant has broad leaves with ridges along its entire perimeter giving it a starburst like appearance. The leafs of the second plant are not waxy but are an even darker shade of green on their top and an even paler light green on their underside compared to the elongated leaf plant.  The leaf of the second plant is divided by green lines that emanate radially from one central line that divides the leaf laterally. The third non-flowering plant appears to have leaves that cluster together to form an elongated structure that is itself leaf like. The individual leaves are oval shaped and emanate from a central stem which branches of the plant's main stem. As you move distally away from the main stem down the side leaved stems the leaves become steady smaller on either side of the stem.

carbon dioxide transport

Submitted by jdantonio on Fri, 03/17/2017 - 10:41

A major cellular byproduct that needs to be removed from the cells of the body and eliminated from the body is carbon dioxide. This is done by the transport of carbon dioxide in the blood and the removal of carbon dioxide by gas exchange in the lungs. There are three major forms which carbon dioxide takes while it is transported out of the body dissolved gaseous carbon dioxide in the plasma, bicarbonate ion in the plasma, and bound to hemoglobin as carbamate in the blood.  The ratio of carbon dioxide forms in the body is dictated by the internal environmental conditions. Normally the body's blood ph is slightly basic at about 7.4 ph, in this state carbon dioxide is driven to form bicarbonate ions through a reaction that is catalysed by the enzyme carbonic anhydrase. In the cell at rest about  85% of all carbon dioxide in the blood is in the form of bicarbonate. If the individual is exercising heavily they lower the ph of their blood, this drives the reaction of towards the  reacts, carbon dioxide, bys le chateau's principle  because of the increase in hydrogen ions in the blood. In either case the exchange of carbon dioxide is driven by a concentration gradient with the surrounding environments, carbon dioxide moves from the cells of the body to the blood because the cells produce carbon dioxide and therefore have a higher concentration than the blood. This drives the carbon dioxide into the blood where it diffuses into blood cells and is converted to carbonate, binds to hemoglobin, or dissolves in the plasma. At the lungs the concentration gradient is reversed, the lungs have low carbon dioxide concentrations as they constantly remove it by exhaling. This drives the removal of carbon dioxide from the blood as gas which in turn drives the conversion of carbonate ions in the blood to gaseous carbon dioxide that can be exhaled. By this process of carbon dioxide conversion to and back from bicarbonate, driven by concentration gradients and lechatelier's principle, a vast majority of carbon dioxide is eliminated.  

 

Geers C and Gros G. 2000. Carbon Dioxide Transport and Carbonic Anhydrase in Blood and Muscle. Physiological Reviews 80(2): 681-715. American physiological society. <http://physrev.physiology.org/content/80/2/681.full-text.pdf+html>. Accessed 2017 Mar 17.  

 

Stanfield CL. 2013. The Respiratory system: Gas exchange and regulation of breathing. In: Stanfield CL, Churchman K, Scharf S, Jones CC, McElroy J, williams A, Cogan D, Tabor N, editors.  Principles of human physiology. 5th ed. Boston: Pearson. p. 473-500.

observations of a cat

Submitted by jdantonio on Fri, 03/17/2017 - 00:31

The organism is approximately one foot long and six inches tall when it walks on all four of its paws. The organism has all white fur which is significantly shorter  on its back and abdomen then on its head and legs. The ears of the organism are triangular and stand upright on its head, they are white and fur covered in the back/exterior and pink and hairless in the front/interior. The organisms left eye is blue with a vertical slit like pupil, while its right eye is green-blue with a vertical slit like pupil. The organism’s eyes are not aligned, the left one points directly forward while the right eye points slightly farther to the right. The organism has a very short face and a pink nose as well as whiskers on its face. The organism is a breed of  Felis catus the domestic cat. The organism has claws on all of its paws and is able to retract these claws back into its paws. The organism has pink pads on the bottom of its feet which consist of one large central pad and three smaller radial pads.  The organism has no teeth in its mouth.

The organism has exhibited the ability to open a door in a house by clawing at the edge of the door until the door is open enough for it to pass through the doorway. The organism tends to fall asleep on its owns, choosing to lay on its owner's chest. The organism has a habit of needing the area which it is about to lay on with its claws, possibly to test the  softness of the surface it is about to lay on. The organism has a loud verbal signal that it uses at apparently random times, neither signalling that it wants food or that it wants any change in its environment. It just stands in the middle of the room meowing at times. The organism does not respond to verbal commands or signals from its owners.  The organism will chase a red dot projected from a laser pointer around a room if the dot is within is view. If the cat catches the red dot it will continually paw at the dot for several seconds before apparently losing interest and ignoring the static dot. When presented with food that is not to the liking of the organism the organism will turn around and make a backward motion toward it with it rear paws as if covering the food with kitty litter in cat box.

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