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Plant Diversity Poster Sections Draft

Submitted by dkotorobay on Wed, 04/26/2017 - 23:34



Plants that exhibit pronounced water storage in one or more organs are generally classified as succulents. There are other characteristics that ensure the plants survival in a water limited environment, this is referred to as “the succulent syndrome”. Hallmark traits of this “syndrome” includes a shallow root system that allows for the rapid uptake of the unexpected rains that are common in deserts; a thick waxy cuticle that prevents excessive water loss, and CAM photosynthesis, which allows plants to uptake atmospheric carbon dioxide at night when water loss is reduced.


Euphorbia milii are native to the island of Madagascar. It is has a woody stem and that is adapted for water storage, it has red inflorescences that are found in clusters called cyathiums. It also produces a poisonous milky sap. 

Euphorbia and Aizoaceae:

The Aizoaceae are a type of old world succulents. The leaves and stems are fleshy and close to the ground and it relies on CAM photosynthesis. The Aizoaceae are a flower producing succulent though the flowers are not produced consistently, there are no spines for protection. 

Euphorbia and Cactaceae:

The Cactaceae are a large and diverse group of stem succulents that are predominantly found in the arid environments of the North and South Americas, they are a combination of old and new world succulents. They have a fleshy stem as opposed to the woody stem of the Euphorbia, but there are spines present, different than those of the Euphorbia milii because the spine on Cacti are modified leaves. Cactaceae also produces flowers or inflorescences on the ends of the growing tips. 

Euphorbia and Didiereaceae:

The Didiereaceae is a new world type of succulent. Euphorbia milii and the Didiereaceae are both found in Madagascar and are the most similar morphologically. The Didiereaceae also has a woody stem with long spines, the way that they differ is the leaves are right next to the spines and there is leaf growth throughout the stem, and there are no inflorescences.

*The Madagascar lemurs climb the Didiereaceae and eat the leaves off the stems.*

Mammalogy: Invent a Mammal

Submitted by dkotorobay on Thu, 04/13/2017 - 23:45

The moose mouse, or more commonly known as the Moomouse, is scientifically named Alces musculus, literally meaning moose mouse. It is similar in body form to the Mouse deer which belongs to the Family Tragulidae and is a chevrotain. Notable differences between the two are their habitats, size including the presence of antlers, and social interactions between members of the species. They are essentially a species similar to the chevrotains that have evolved the morphological novelty of antlers, which are typically not seen on smaller mammals, thus making the Moomouse unique in its phylogeny.

            The Moomouse lives in temperate deciduous forests located in places such as the east coast of North America, parts of eastern and central Europe, as well as some of southeast Asia. The temperatures here range from -30°C to 30°C and there are four seasons, with a rainfall of between 750 to 1,500 mm per year (Przyborski). The terrain is relatively flat with some sloping hills. Their environment causes them to have an herbivorous diet and their dentition reflects that with selenodont molars and no upper incisors, specialized for grazing (page 68, Lab Manual). To avoid their predators, they have adapted to becoming largely nocturnal and they manage to escape them by speeding along diminutive trails into dense vegetation, to break down the plant materials they consume they have a four-chambered stomach and a large cecum (Vaughan et al., page 348). 

New Animal Idea

Submitted by dkotorobay on Fri, 04/07/2017 - 13:09

The moose mouse, or Moomouse, lives in wooded areas and are found in Northeastern America and through out Canada.  They are essentially a species of rodent that has evolved the morphological novelty of antlers, which are typically not seen on smaller mammals, thus makes the moomouse unique in its phylogeny. They have lengthened claws to grab onto trees or use for protection purposes if their antlers are growing at that moment. They have normal fur growth but a reduced sensitivity to cold. The moomice are about the size of regular mice, with the males having miniature antlers so they can defend their territories, fight predators, and attract mates. All moomice have modified claws as a means for climbing up trees and using them as weapons if necessary. They also have fur growth and reduced sensitivity to cold so they could survive the winters. All these traits combined form the moomouse.

The moomouse antlers are only part of the males, so they could fight for territory, fight off predators, and attract mates. The larger and more symmetrical the antlers were the more attractive they are to mates, and the less chance that they will be challenged for their territory.

The process of antler development of the moomouse is like that of a red deer and involves insulin-like growth factor I (IGF-I) which is an important systemic regulator of the pedicle formation as it stimulates proliferation of osteogenic cells from all four ossification stages. Growth factors include epidermal growth factor (EGF) which stimulates cell growth, proliferation and differentiation by binding to the EGF receptor (Price et al.), fibroblast growth factor 2 (FGF-2) and vascular endothelial growth factor (VEGF), and their receptors FGFR1, FGFR2 and FGFR3, and VEGFR-2 respectively. Both signaling systems are widely expressed in the integument and osseocartilaginous compartments. FGF-2 was found in the same cells as all three FGFRs, indicating that FGF signaling may be principally autocrine. FGF-2 induces expression of VEGF, to stimulate and maintain high rates of neovascularization and angiogenesis, thereby providing nutrients to both velvet and bone as they rapidly grow and develop. Bone morphogenetic proteins (BMPs) 2, 4 and 14 and the BMP receptors BMPR1B and ACTRII are also present. These growth factors signal between the osseocartilaginous and skin compartments of the primary antler (Price et al.). These different proteins and growth factors work together in the formation of antlers.

            The development of lengthened claws come in handy for the moomice when they have to fight for territory, climb up trees, or ward off a predator. The development of a longer claws is achieved through a three-part process. The first part is an epithelial thickening for an epithelial appendage, this placode formation is observed before the formation of hair follicles. Successful placode induction depends upon the inhibition of BMP4 expression by noggin. WNT-7A expression is vital for correct orientation of the placode along the dorso-ventral axis; in mice lacking normal WNT-7A function the footpads form on the dorsal instead of the ventral surface of the digit tips and this causes the claws to shortened. The second part involves formation of the claw fold and specification of cells forming the germinal matrix. Evidence from feather and hair development indicates that sonic hedgehog (SHH) plays an important role in elongation of feathers and hair, so SHH is therefore also likely to be important for development of the claw fold. In the third part of claw development MSX1 and MSX2 expression affects the length of the claw by regulating the proliferation of cells in the germinal epidermal matrix. These MSH-like genes play an important role in cell proliferation since their expression is associated with regions adjacent to the progress zone of developing limb buds. During skin development MSX1 and -2 often show overlapping, but not identical, expression domains in regions where active cell proliferation takes place. MSX1 expression maintains cells in a proliferating, “dedifferentiated,” state. In contrast, MSX2 has the opposite role of limiting cell proliferation and accelerating differentiation. Overexpression of MSX2 in mouse hair follicles leads to an increase in the number of cells passing from a proliferating stage to a differentiating stage, whereas MSX2 deficiency in mice produces a marked lengthening of the claws (Hamrick). So this means by reducing the expression of MSX2 the claws on the moomice are lengthened.

The moomice have brown fur to better blend in with their woodland environments. The brown color of their fur is caused by the binding of alpha melanocyte stimulating hormone (a-MSH) to the MC1R protein, which in turn increases the levels of cyclic AMP which causes tyrosinase to be expressed with the result being eumelanin (NIH). To get the brown pigment the agouti protein needs to inhibit the binding of a-MSH for short periods of time so that some phaeomelanin is expressed as well, and the fur is a mix of mostly eumelanin and some phaeomelanin to appear brown. They also have the TPVR3 gene that reduces their sensitivity to the cold and allows them to survive through the winter (Callaway), which is an advantage as winters in Northeastern America can be brutal.

Works Cited

Tissue Cell. 2007 Feb;39(1):35-46. Epub 2007 Feb 20.

The distribution of the growth factors FGF-2 and VEGF, and their receptors, in growing red deer antler.

Lai AK, Hou WL, Verdon DJ, Nicholson LF, Barling PM.

Journal of Anatomy Volume 207, Issue 5, November 2005, Pages 603–618

Deer antlers: a zoological curiosity or the key to understanding organ regeneration in mammals?


J. S. Price, S. Allen, C. Faucheux, T. Althnaian, J. G. Mount

MC1R gene, Melanocortin 1 Receptor, National Institute of Health: US National Library of Medicine, reviewed March 2007, Published December 21, 2016

Mammoth genomes hold recipe for Arctic elephants, Ewen Callaway, Moodle Site

Development and evolution of the mammalian limb: adaptive diversification of nails, hooves, and claws, Mark W. Hamrick, First published: September 2001


NeuroBio Write Up #3

Submitted by dkotorobay on Wed, 03/29/2017 - 12:44

Title: Restoring Natural Sensory Feedback in Real-Time Bidirectional Hand Prostheses

Main Points:

-Amputees with the current prosthetics are not provided with the “rich sensations that we naturally perceive when grasping or manipulating an object”.                                                          - “Ideal bidirectional hand prostheses should involve both a reliable decoding of the user’s intentions and the delivery of nearly “natural” sensory feedback through remnant afferent pathways, simultaneously and in real time.”


The use of transversal multichannel intrafascicular electrodes to stimulate the median and ulnar nerve fascicles. TIME implants were placed into the median and ulnar nerves of an amputee’s residuum. The participant was then tested on their ability to modulate the grasping strength by measuring the force output with a pressure sensor. There was a high possible number of trials n>700, data was acquired in several sessions distributed in 7 days. Data was considered an outlier if it exceeded 2 SDs from the mean.


-It appears only 1 test subject was used, this is not a large test group, if more participants had been used this would validate the results more than just having positive results from one participant.

-The implantation process is invasive, there is always the possibility that the nerves could be damaged in the implantation surgery.

-The tests ran for as long as the participant was comfortable, there were no set repetitions or times for the experiments.

-Trials were interrupted when the subject requested.


Figure 1: a) It shows the finger sensory readouts as S and the stimulation current as I and it then has another graph that is plotted as I on the y-axis and S on the x-axis. Show that the minimum and maximum for S correspond with the I minimum and maximum. b) It is a photograph of the insertion of a TIME electrode in the medial nerve of the participant, done surgically. c) Another photograph showing the participants ulnar nerve with two implanted electrodes. d) A graph that has data of the index and little fingers and their reported threshold and saturation of sensation over 4 weeks. With injected charge on the y-axis and week on the x-axis. e) Another graph showing the sensation strength of each finger on at 1-10 scale over the 4 weeks. These graphs have reported strength on the y-axis and injected charge on the x-axis.

Figure 2: a) 3 graphs of the little finger and 3 of the index finger side by side showing the results of object pressure, finger sensor, and stimulation current over the course of a minute, this data is representative of 200 trials. b) Again, data of the little and index finger, this time showing matrices of results for requested force versus exerted force, followed by a graph of overall performance. c) A comparison of performance of the prosthetic hand with visual, without visual and a healthy arm. d) A confusion matrix for force control task with a palmar grasp, 111 repetitions in 2 sessions.

Figure 3: a) A test that was like the experiment in figure 2A but it was a placebo trial. The participant was asked to apply the minimum level of force but with no electrical stimulation. b) The confusion matrices of the requested versus preformed force levels of the index and littles fingers at different velocities.

Figure 4: a) Graphs showing the results of the participant preforming three task repetitions with an object in different location on the palm. b) A confusion matrix showing the accuracy of the grasps. It was at a 97.3% mean accuracy.

Figure 5: a) and b) show stiffness recognition, discrimination, and accuracy tasks. a) shows the hand control decoded from sEMG activity and index finger robotic hand sensor readout. b) shows the confusion matrix of the accuracy and performance over three sessions.

 c) and d) show shape recognition, discrimination, and accuracy analysis. c) Graphs that show the decoded motor commands, sensor readouts and stimulation amplitude. d) The confusion matrix that assessed task accuracy.


Would an experiment like this be possible for an amputee that had an amputation about the elbow? What about an above the knee amputation? How would the experiment be different if there were no joint right about the amputation? How well do the fingers in the prosthetic move?


Prosthetic movement, Movement of prosthetic via transversal multichannel intrafascicular electrodes, stimulation of median and ulnar nerve fascicles to facilitate prosthetic movement. 

NeuroBio Write Up #2

Submitted by dkotorobay on Fri, 03/24/2017 - 11:46

Title: Red-shifted channelrhodopsin stimulation restores light responses in blind mice, macaque retina, and human retina

Main Points:

The question the paper is trying to answer is whether or not using red-shifted channelrhodopsin to treat degenerative blindness will work as it did in mice.

This study is important because it could possibly be a way to treat vision loss caused by retinal degeneration.

The results were that red-shifted channelrhodopsin also drives neuronal responses in macaque retinae as well as in the central human retina, the site of high-acuity vision, demonstrating the therapeutic potential of the red-shifted channelrhodopsin molecule.


The models used were rd1 mice, macaque retinal explants and humans.

The techniques:

For the blind mice AAV2 injections through the sclera.

For the primates they were terminally anesthetized and their eyes were removed and the retina was isolated from the vitreous humor and cut into 1 cm pieces. The retinal explants were infected with the AAV2 and AAV8 until the day of electrophysiological recordings or fixation, the AAV infections were performed within 2 hours of the retina explants being put in tissue culture.

 For the human experiments postmortem human ocular globes were acquired from the school of surgery, 6 donors, 63 – 95 years old, postmortem delays 9 – 38 hours. Similar proceedings to the primate experiment.


The age range constrained to older ages in humans, the pool of human subjects was small, only 6 people. There were also no live subjects after the mice. This may be an ethical issue.

The controls were appropriate, they tested multiple models in the same manner, though the mice were alive and the primates and humans were not alive.


Figure 1: 3 panels, showing that the channelrhodopsin can be efficiently targeted to the RGC membrane and dendritic arbor of blind mice.

Figure 2: Graphs showing the responses triggered by optogenetic stimulation of the retina.

Figure 3: Different types of graphs showing the triggered responses in the blind mice that were treated with the AAV2.

Figure 4: One of the figures shows the locomotive behavior of the blind mice before and after treatment as well as graphs that correspond with those results.

Figure 5: Graphs showing the light responses in the AAV-infected primate retinae.

Figure 6: I believe these graphs and pictures are demonstrating where and what is activated when the explant has been infected with the AAV.

Figure 7: Pictures of the retina showing part of the foveal pit.

Figure 8: AAV- mediated optogenetic activation of the human retina after it had been incubated for 12 days.


How would such an experiment work on a live human? Would it be conducted more like the mouse experiment?


Treating degenerative blindness, channelrhodopsin used to treat vision loss

Mammalogy Notes Part 1

Submitted by dkotorobay on Fri, 03/24/2017 - 11:05

Ungulates: mammals with hooves. Claws, nails, and hooves: unguis- keratinized. subunguis- transition to skin. pad- skin (may be sensitive). There are two orders of ungulates: order Perissodactyla: odd-toes ungulates, order Artiodactyla: even-toed ungulates. Order Perissodactyla: mesaxonic foot, order Artiodactyla: paraxonic foot. (the astragalus is called the talus in humans). Convergent adaptations for cursoriatlity (running): the development of the astragalus as the main weight bearing bone (the calcaneus in humans), reduction/fusion of the metapodials into a cannon bone. The shape of the astragalus in perissodactyls and artiodactyls: O. Perissodactyla: top surface pulley-shaped, bottom surface is flat. Limits movement between the leg and ankle to flexion and extension. Less mobility between ankle and foot, limits movement to flexion and extension. Shared derived characteristics: enlarged astragalus with pulley-shaped upper surface only, mesaxonic feet with a reduction of digits, all are hindgut fermenters (enlarged caecum with commensal bacteria). Family: Tapiridae- tapirs (Tapirus): they are morphologically primitive: unspecialized limbs, primitive tooth number (44), simple loph pattern to teeth (like rhinos). They have: reduced nasal bones, elongated proboscis formed by nose and upper lip. They generally live near swamps, rivers or other wet areas where they eat succulent plant material and fruit, all are either endangered or vulnerable, all pops. are decreasing. Family: Rhinocerotidae: Live in a variety of habitats but need permanent water, prefer to eat leaves and grass but will eat woody vegetation and fruit. Diceros bicornis (black African and Asian rhinos): pointed, prehensile upper lip for browsing. Ceratotherium simum (white African rhino): square lip for cropping grasses (grazing). Behavior: solitary or mom/offspring groups, females breed at 5/6 years, males at 10, usually a baby every 2-4 years. Horns: mass of long hair-like fibers fused together, composed of mineralized keratin with no bony core or sheath. Family: Equidae: the most cursorial perissodactyl: calcaneum is long and posteriorly placed, astragalus is weight-bearing, foot greatly elongated, only 3rd digit is functional. All equids are grazers. Behavior: polygynous (1 male, many females), strong social hierarchy- led by single stallion., herds based on extended family groups/ “clans”, social structure regulated by complex behaviors and vocalizations. The development of grasslands in the early Miocene is thought to be the driving force behind the evolution of horses. Were highly diverse in the past, Baluchitherium (Peracetatherium), from the Oligocene of Pakistan, is the largest known land mammal. Megacerops (Brontops) was the equivalent of a forest elephant in the late Eocene of N. America. 

Lab Report Genetics

Submitted by dkotorobay on Mon, 03/06/2017 - 14:48


This paper focuses on the mutations in genes in the adenine that induce a red color in yeast. The mutations were induced with a UV light and then the yeast colonies were allowed to grow on a nutrient rich media. After sufficient growth time was allowed the yeast was then transferred to nutrient poor media without adenine to see if nutrient availability would affect color. In addition, the yeast was also transferred to a nutrient poor media with adenine to determine if the mutations involved adenine or if the mutations were caused by a different gene. The results showed that mutations can be induced through UV radiation and then when these mutations are crossed with other mutations and controls it is evident which mutations did or did not involve mutations in the adenine.


Mutations are random changes in the base code of a DNA molecule, they are the ultimate source of genetic variability. Some of the time mutations will result in a change of phenotype. Visible mutations are rare events because of DNA’s ability to replicate without mistakes is near perfect but occasionally mistakes in replication do occur. The chances of finding a specific mutation are little to none. It is possible to increase the occurrence of them by various mutagens such as chemicals, x-rays, or ultra violet radiation (Loomis, Mutation Protocol 1).

The experiment conducted had three parts. The first part was to induce mutations using UV-light, the second part is to screen for mutations, and the last part is to categorize the mutations by complementation testing.

Exposure to UV radiation was the method used to produce mutations in haploid cells, but even with exposure to radiation mutation is still a random event so looking at multiple yeast colonies to find specific mutations is necessary. The results from the two class sections were pooled to obtain the five mutations that were found.

Screening was done through visual examination. Looking for mutated yeast that should have been red or pink. Yeast strains from the opposite mating type were also exposed to UV-radiation so that the resulting mutants could be crossed, one class section induced mutations on the “a” mating type and the other class section on the “a” mating type.

When the two mutant strains are crossed the F1 generation is analyzed. If the F1generation expresses the wild type phenotype, it can be concluded that each mutation is in one of two possible genes necessary for the wild type phenotype. When it is shown that genetically two or more genes control a phenotype, the genes are said to form a complementation group. On the other hand, if the F1 generation does not express the wild type phenotype, but a mutant phenotype instead it can be concluded that both mutations occur in the same gene (

By observing the results of the F1 generation in the mutant yeast crosses conclusions will be drawn on whether complementation occurred or if both mutations to the DNA occurred on the same gene.


Methods Project Introduction

Submitted by dkotorobay on Wed, 03/01/2017 - 11:50


This experiment was conducted to see what, if any, differences were to arise from instructions written by one student and followed by another. Instructions were written and then assigned to another student to follow. In the instructions it was required to take three pictures. One being a close up of moss showing and labeling the sporophytes and gametophytes, another showing the general location of where the moss was found with an arrow pointing to the moss, and the last picture was to be an aerial view of the area, either on Google maps or Google Earth, with an arrow on the map pointed to where the moss can be found. The next part of the experiment was to create a composite image, the student following the instructions was unable to ask for clarification on any point and was then required to recreate the composite image. The resulting image was then compared to the original image to see what differences there were. The author of the instructions then had to speculate as to why the differences occurred and what could have been more clear in the methods or any other reasons that could have caused differences between the images.  

NeuroBio Lecture 2/27 Part 2

Submitted by dkotorobay on Tue, 02/28/2017 - 13:20

A good question is how do tatse signals get to our brain. And the answer is through the cranial nerves 7, 9, and 10, not through the spinal cord. The gustatory nucleus is in the medulla, there are additional  projection to salivation adn vomiting centers. The ipsilateral VPM thalamus is also involved. And the primary gustatory cortex is where the concious perception of taste occurs. Taste information shares bandwidth as it travels. Individual taste receptors are very specific, multiple taste receptor cells within a papillae may synapse onto a primary taste axon, it reduces the overall number of required neurons, enables the flexibility for new tastes within the system, neurons broadly identify tastes. It is not a 1:1 ratio for neuron to taste. A collectively activates population encodes specific taste, the response pattern is the same as population coding. 

Smell and odor identification adds a dimension to taste for identifying foods and it can help warn about danger. Many soecies produce chemical ordors for social communication called pheremones. Pheremones are used for reproductive behavior, marking territory, identification, and agression or submission. The olfactory epithelium cells detect odorants, they are supporting cells that produce mucous to dissolve odors. They are basal cells that continually produce new receptor cells every 4-8 weeks. Odorant receptors make up about 3-5% of the mammalian genome, in humans that about 350 receptors and more than 1000 receptors in rodents. This involves GPCRs, one in particular is important, Golf, or the olfactory specific Gprotein, which involves cAMP gated ion channels, which requires cation and chloride channels to depolarize. Receptors show adaptation after continuous stimulation. Which means that after you've been around a scent for a while you get acclimated to it you can't smell it anymore. 

Odor signal transfer works by first having the scent come in contact with receptor cell axons then moving on to the cribriform plate next going to cranial nerve 1 and lastly reaching the olfactory bulb. 

Olfactory pathways start when receptor cells respond to many odorants, odorants can activate many receptor types. Olfactory axons converge on glomeruli in the olfactory bulb, and the glomeruli recieve inputs from 1 type of receptor, called local modulation. The central olfactory pathway refers to when the olfactory tracts goes directly to the forebrain, including the olfactory tubercle and primary olfactory cortex, also known as the temporal lobe. It reaches the thalamus before the association areas. 

There are two types of population coding. Spatial and temporal. Odors show sensory maps, and different odors activate different populations. Temporal coding involves differential spike timing and within and across sensory maps. There is still a lot of information to the decode, which occurs in oscillations. 


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