User:Hobbscassidy/sandbox

Shared Sandbox - Salamander

Individual Thoughts
General additions for the Comparative Anatomy page Specific Additions for Comparative Anatomy
 * History of comparative anatomy was long winded and vague. Galen section read like a story..
 * Limited Citations, only four, mostly book like sources
 * general grammatical errors
 * Long run on sentences
 * Good definitions for homology and analogy (might seem like textbook language), addition of homoplasy
 * Natural scalae deviation added?
 * Add a section of phylogeny
 * describing the characteristics versus genetic data more thoroughly
 * Form and function and how that relates to Darwin's theory of natural selection and descent with modification
 * categorization?

Collective thoughts
I was a little confused about the article's description of the role of genomics in comparative anatomy. I think this could be cleared up by adding a section on phylogeny and explaining that the trees are made from genetic data, but the physical characteristics derived from anatomical structures is mapped onto those trees. I think is an important aspect because it shows the relationships between species, which is a large part of comparative anatomy. This addition could be expanded upon to list some of the major groups and taxa that are being studied.

This could tie into another section on form and function that relates to the homologous and analogous definitions on the page.

Addition to a Page
Homoplasy Definition

Homoplasy is a subcategory of analogy, where structures look similar, but are derived from convergent evolution, meaning that the two organisms displaying homoplasy do not share a common ancestor. Instead, they may have evolved in common environments and the traits arose due to natural selection.

Organism Choice
Sparrow - I would be interested in dissecting a bird, mostly because I haven't ever dissected one before, and I am intrigued by their bone structure. I have always been super interested in how birds give up duplicates of organs in order for flight to be possible and would like to see that in a bird. Microbat - Not a lot of anatomy present on page, plenty of room for addition. Additionally the larger Bat page lacks information on microbats. I am really intrigued by echolocation and how that play a role in the other sensory organs present in bats. Mudpuppy - Mudpuppy page Necturus lacks anatomical information, and information in general. I really am interested in mudpuppies because of their aquatic nature, because of their relation to the salamander they are and how they play a role in the transition to a terrestrial lifestyle.
 * Passerine - limited anatomy, specifically focused on the foot, legs, and feathers, not much on organs.
 * passer - also has limited information.
 * not a page, but the preglossae is mentioned as a bone in the tongue and that seems pretty interesting.
 * Bat - Specifically the section on echolocation, sensory organs, and organ placement. The microbat page could also be edited, but many parts of the microbat link to the bat page.
 * Common mudpuppy page has a lot of started sections that lack depth, and no large section on anatomy.
 * The section on reproduction is also interesting and not very extensive.

Cassidy
- paedogenesis: lacks a metamorphosis stage that is common in amphibians. The larval stage will grow to the adult size, and the gonads will mature while the organism is still aquatic. This applies to the mudpuppy in general - not a specific topic that we are addressing, but that keeps coming up in individual topics.

-Mouth and teeth: Two different sets of conical shaped teeth, underdeveloped tongue, inertial feeding

Josh
Game Plan for the Mudpuppy (cont'd; Josh Hoare's entry) https://ag.purdue.edu/fnr/discover/HerpetologyLab/Documents/Ultsch_GasExchange.pdf
 * Respiratory system - Mudpuppies have the capability of breathing through larval-gills that are retained as adults
 * External gills - paedomorphic feature retained throughout maturity by Mudpuppy that is not seen in many amphibians
 * Possible beginning of adaptation present in embryonic stage to fight against hypoxic environments

Jacob
Game Plan for Mudpuppy (Jacob Beck entry):
 * Mucous and Granular Glands: used for thermoregulation, defense, etc. secretes mucous that covers the body environmental protection. Granular glands are for venom and self defense.

Cassidy
Edits - Editing Diet section, maybe a subheading for teeth?
 * Teeth are strictly for grasping prey, they do not have a crushing function. This means that mudpuppies swallow their prey whole, limiting the size of the prey. Additionally, they do not have facial muscles along the upper jaw. This could lead to the digestive tract as a whole and how efficient their digestion of whole prey is.
 * They have 3 different sets of teeth- dentary teeth, premaxillary teeth, and vomerine teeth, but all the teeth are small and conical, indicating that mudpuppies are homodont
 * The article itself lacks any detailed information about the teeth, and limits its discussion to the diet of the mudpuppy. The article does not address how the teeth are used, or the other impacts that affect feeding - immovable tongue, no upper jaw fascial muscles, and "suck and gape" feeding style
 * Talk page post - I think an interesting addition to the diet section of this page would be to elaborate a bit more on the different ways that the aquatic salamander use their teeth and their feeding technique. Aquatic salamanders use a type of inertial feeding that involves grasping the prey with their teeth and quickly sucking in water, inertial feeding. Also maybe adding more detail to the anatomy of the mouth and teeth including the underdeveloped tongue

Salamanders have three different sets of teeth: dentary, premaxillary, and vomerine teeth, which are named due to their location in the mouth. All the teeth, despite their different locations, are very similar. They are small and conical, meaning that salamanders are homodonts. Aquatic salamander teeth are used to hinder escape of the prey from the salamander, they do not have a crushing function. This aids the salamander when feeding. When the salamander undergoes the "suck and gape" feeding style, the prey is pulled into the mouth, and the teeth function to hold the prey inside the mouth and prevent the prey form escaping. The prey is fully brought into the mouth with the water flow.

Jaw Anatomy - The jaw of a mudpuppy is considered metaautostyly, like most amphibians, meaning that the jaw is more stable, and the salamander has a dentary. This affects their diet by limiting the flexibility of the jaw to take in larger prey.

Josh

 * The Salamander page, under its section about description, only lists a section concerning the "trunk, limbs and tail," and contains no anatomical information on anything skeletal, or relating to organs. This section could be broken up into external and internal features, with external features focusing on the skeletal and organ-related specifics to salamanders.
 * Most salamanders have both thyroid and parathyroid glands; the common mudpuppy does not have a parathyroid gland. The thyroid gland in some salamanders, like the Axolotl, produce normal thyroid hormones, but cells in the organism express thyroid hormone receptors (TR) that are mutated, and do not bond correctly with thyroid hormones, leading to some salamanders in a state of perpetual juvenile-hood.

Useful Citations
Gill Musculature Terminology

Axolotl Thyroid Research

Jacob
Granular and Mucous Glands

Amphibians possess two types of glands, mucous and granular (serous), both of which are structurally different and exhibit vast differences in function. Both of these glands are considered cutaneous and are composed of three different sections which all make up the gland as a whole. These sections include the first the duct, then the intercalary region, and lastly the alveolar gland (sac). Structurally, the duct is derived via keratinocytes and passes all the way to the outer region of the epidermal skin layer, allowing external secretions of the body. The gland alveolus is the basal layer of the granular gland located in the stratum sponganium with cell layers specializing in secretion. In between the alveolar gland and the duct is the intercalary system which can be summed up as a transitional region connecting the duct to the grand alveolar beneath the epidermal skin layer. In general, granular glands are larger in size than the mucous glands, however mucous glands hold a much greater majority in overall number.

Granular glands can be identified as venomous and often differ in the type of toxin as well as the concentrations of secretions across various orders and species within the amphibians. They are located in clusters differing in concentration depending on amphibian taxa. The toxins can be fatal to most vertebrates or have no effect against others. These glands are alveolar meaning they structurally have little sacs in which venom is produced and held before it is secreted upon defensive behaviors.

(need to include information regarding structure).

Mucous glands are non-venomous and offer a different functionality for amphibians than granular. Mucous glands cover the entire surface area of the amphibian body and specialize in keeping the body lubricated. There are many other functions of the mucous glands such as controlling the pH, thermoregulation, adhesive properties to the environment, anti-predator behaviors (slimy to the grasp), chemical communication, even anti-bacterial/viral properties for protection against pathogens.

Peer Review
Great work! I really like the collaboration on your group page and how well organized it is. For Cassidy: I believe your topic is the mouth and teeth? I think that is nice straight forward anatomical area to study. The only suggestion I would have, as it may be helpful to your group, is to have a hyperlink to the page you plan on editing. For Josh: The sources you found are quality. There will be plenty to add on to the salamander page for organs and skeletal systems. For Jacob: Nice work so far, you have some really well formed ideas written out already. Are you adding the info on glandular and mucous glands to the salamander page? It wasn't quite clear were the written information was going to end up. As I suggested to Cassidy, it could be helpful to add a hyperlink to the page you plan on editing. Good job guys.Benson02 (talk) 04:51, 25 March 2017 (UTC)

Cassidy - Reflected in Draft 1, edits

 * Shawn - I will add the citation for teeth, as well as changed the wording, as well as for the inertial feeding mechanism. Still looking for a more detailed overview of the mudpuppy teeth.
 * Riley - I am definitely looking into more detailed information on the mudpuppy jaw and musculature, however that information is difficult to track down.
 * Joe - Thanks for the suggestion!
 * Grant - Reformatted according to your suggestion, thanks! For other comments see above
 * Andrew - Working on finding new sources/ other sources right now. It would be really interesting to compare and contrast the teeth.
 * Lexie - Yes, I totally agree. I think I may be also leaning toward adding information on the jaw of the salamander in light of recent class topics.
 * Liz - I was thinking that adding a section on jaw anatomy would be really interesting as well, thanks for the suggestion. I haven't quite delved super deep in to the mudpuppy diet, but I will add to that section.
 * Chris - I will definitely add that hyperlink
 * Blanca - I added where it could possibly fit, I haven't quite figured out where I think I should put it because the jaw anatomy runs into the teeth which runs into the diet section...

Joshua - Reflections to Peer Responses

 * Shawn: Thanks for the suggestion, integrating them is something I will for sure do.
 * RIley: I agree that the phrasing is somewhat vague and is definitely something I will address in the near future. I wanted to add citations in a later draft, but I see now that I should have just added them in the first one. Adding a picture of the thyroid (if I can find it!) is something I planned on doing.
 * Joe: Citations, as stated previously, are a point of emphasis. I'll have to ask you how you would rephrase it, but I see what you're saying!
 * Grant: Commenting on the skeletal system would be a good addition to my draft, I agree. Thank you!
 * Andrew: My plan was to just focus on the musculature of the external gills and the thyroid gland, but as I continue to research, perhaps it would be a good idea to look deeper into other internal mechanisms of paedomorphosis in the mudpuppy. Looking at the benefits of not possessing a parathyroid gland was an avenue I had not thought of, and will definitely keep it in consideration as I move forward in the drafting process. Killer points, dude!
 * Lexie: Yes, the intent was to post my edit on the salamander page! I will be sure to keep an eye out for if there are any replacement organs for the parathyroid gland.Liz: My first draft is very rough, surely, but your points are appreciated. As I go further into the draft process, I will definitely make sure that the language does not become too advanced for the general Wikipedia audience. I will definitely have to go over the Wikipedia tutorials on adding images, as that was something I planned on doing. Thank you for your input!*Chris: Thank you for your comment!
 * Blanca: I will cross reference the extent to which salamander skeletons are touched upon in the more general pages (amphibian, etc.) to see if there would be merit it adding skeletal information to the salamander page. Advantages or disadvantages to the presence/absence of the parathyroid gland tie in nicely with the current function/lack thereof in reference to the thyroid in mudpuppies, so I will be sure to keep this is mind as I move forward in the drafting process!

Jacob - Reflections to Peer Responses for Draft One:

 * Shawn - Thank you for the response, sounds like I need to add further citations beyond what I have given as well as increasing my overall fluency.
 * Riley - I will reduce my vague language and work to provide concrete examples where needed. I also plan on creating two completely different sections for the mucous and granular glands. They are both glands but both differ significantly in their overall functionality for amphibians.
 * Joe - Believe it or not that single source gave me ALL of that information. No worries though, I have two other stellar sources in which I will add more material regarding structure and functionality/mechanisms of the glands. Good looks though, I wouldn't want to accidentally plagiarize. I appreciate you looking out!
 * Grant - Thank you for the suggestions, I more or less just plotted down information as I came across it in the article. I will definitely restructure it for fluency sake. More citations are to come, I have 2-3 I am ready to add.
 * Andrew - With further research I have come to the conclusion that mud-puppies (at least not the one we are dissecting) do not seem to have granular glands, however they certainly do possess mucous glands. I plan on creating a new page for mucous and granular glands and then hyperlinking it to the "Amphibian" page.
 * Lexie - All of my information will most likely end up on a whole new page for Mucous and Granular glands altogether. Then I plan on hyperlinking it to the Amphibian page overall as the not all mudpuppies possess granular glands from my understanding. I feel this topic would be best associated with amphibians.
 * Liz - I definitely plan on adding images for both mucous and granular glands. I need to look over the wikipedia training segment that gives the tutorial on providing/adding proper images with citations as I want to avoid stealing credit for other's works (plagiarism). This is great advice and certainly merits addition to my article!
 * Chris - This is a little bit tricky as I will need to talk more with Dr. Schutz regarding where my material will ultimately end up. I posted on the amphibian talk page requesting if I should create a whole new page specifically for Mucous/Granular glands as they pertain to amphibians. They gave me the "go-ahead" to create a new page altogether...so this will require some careful planning.
 * Blanca - I plan on creating a whole new page as I was given the "okay" from the main Amphibian talk page to do so. I need to collaborate with Dr. Schutz to make sure I execute this process so it is both effective and appropriate.
 * Dr. Schutz - I was given the "okay" from the Amphibian talk page to create a new page altogether for the Granular and Mucous glands. There is already a mucous gland page present on wikipedia so I will have to meet with you and discuss how I will either add information for mucous glands as they pertain to amphibians specifically or create a new page and link it to the Amphibian page (same goes for granular glands). I can also hyperlink some vocabulary terms as Joe pointed out thoroughly in his review. I am in the midst of adding more sources and compiling information regarding the overall structure of both glands as we have covered a bit of this material in class so far. I plan on referencing and citing our textbook (it has good information on both glands) and I have just added a citation from the Journal of Morphology in the group response as it focuses on the Necturus integument. I need to start looking for images that pertain to both glands as well as review the wikipedia training that discusses proper image citations. In summary I need to fix fluency, structure/organization, add citations + images, and polish my work so far.

parathyroid/ thyroid

 * Here is a citation for the paedomorphosis due to lack of thyroid hormone. The Introduction covers a brief intro to paedomorphosis and neoteny due to thyroid in salamanders.

glands

 * Here is another citation for the antimicrobial function of mucous glands, it's a little more detailed than necessary, but if someone on wikipedia is interested...
 * A citation from the Journal of Morphology which specifically pertains to the Necturus Integument. A thorough source for Mucous and Granular glands...

teeth/ jaws/ diet
Lab manual citations

Cassidy
Salamanders have three different sets of teeth: dentary, premaxillary, and vomerine teeth, which are named due to their location in the mouth. All the teeth, despite their different locations, are very similar. They are small and conical, meaning that mudpuppies are homodonts. Aquatic salamander teeth are used to hinder escape of the prey from the salamander, they do not have a crushing function. This aids the salamander when feeding. When the salamander undergoes the "suck and gape" feeding style, the prey is pulled into the mouth, and the teeth function to hold the prey inside the mouth and prevent the prey form escaping. The prey is fully brought into the mouth with the water flow.

The jaw of a mudpuppy also plays a significant role in its diet. The mudpuppy jaw is considered metaautostyly, like most amphibians, meaning that the jaw is more stable, and the salamander has a dentary. This affects their diet by limiting the flexibility of the jaw to take in larger prey. (Possibly an image here)

Neoteny in mudpuppies - The common mudpuppy never leaves its aquatic environment and therefore does not undergo morphogenesis. Amphibious salamanders that do have a morphological transition exhibit many different changes, including the loss of external gills and the development of heterodont teeth. (Deciding whether this is relevant, maybe on the necturus page) Once morphogenesis occurs, mudpuppy vomerine teeth take on a more bicuspid shape.

Diet - Broad description of diet found, not unlike what is already present in the page. Some articles have mentioned that salamanders also ingest fish eggs which can have implications for the fish in the future years.

Gameplan
Adding section on teeth of the common mudpuppy to the mudpuppy page. That will link to the necturus page to go into more detail on the change that can occur when metamorphosis occurs. This in turn will link, so will the mudpuppy page, to dentition in general.

Common Mudpuppy Teeth Salamanders have three different sets of teeth: dentary, premaxillary, and vomerine teeth, which are named due to their location in the mouth. All the teeth, despite their different locations, are very similar. They are small and conical, meaning that mudpuppies are homodonts due to their similar shape. Aquatic salamander teeth are used to hinder escape of the prey from the salamander, they do not have a crushing function. This aids the salamander when feeding. When the salamander undergoes the "suck and gape" feeding style, the prey is pulled into the mouth, and the teeth function to hold the prey inside the mouth and prevent the prey form escaping. The prey is fully brought into the mouth with the water flow.

Picture inserted in diet section.

The jaw of a mudpuppy also plays a significant role in its diet. The mudpuppy jaw is considered metaautostyly, like most amphibians, meaning that the jaw is more stable, and the salamander has a dentary. This affects their diet by limiting the flexibility of the jaw to take in larger prey.

Original plan was necturus, however that page seems purely taxonomical (Information on the salamander page; general info on mudpuppy and link to salamander page)

The common mudpuppy never leaves its aquatic environment and therefore does not undergo morphogenesis. Amphibious salamanders that do have a morphological transition exhibit many different changes, including the loss of external gills and the development of heterodont teeth. The teeth become biscuspid shaped that allows the salamander to better grasp its prey. This information was already present on Salamander page, but I added a section under mudpuppy and linked it to the Salamander page.

Teeth in general - Amphibian sub section?

No amphibian section present - created and added between fish and reptiles

All amphibians have pedicellate teeth which are modified to be flexible due to connective tissue and uncalcified dentine that separates the crown from the base of the tooth.

Most amphibians exhibit teeth that have a slight attachment to the jaw or acrodont teeth. Acrodont teeth exhibit limited connection to the dentary and have little enervation. This is ideal for organisms who mostly use their teeth for grasping, but not for crushing and allows for rapid regeneration of teeth at a low energy cost. Teeth are usually lost in the course of feeding if the prey is struggling. Additionally, amphibians that undergo a metamorphosis develop bicuspid shaped teeth.

Gameplan
Insert neoteny subsection in the 'appearance' portion of the Common mudpuppy page. Insert more information about external gills in the 'other vertebrates' section of the salamander page.

Mudpuppies are one of many species of salamanders that fall to undergo metamorphosis. Most hypotheses surrounding the origin of Necturus 's lack of metamorphosis concern the effectiveness of the thyroid gland. The thyroid gland in some salamanders, like the Axolotl, produce normal thyroid hormones (THs), but cells in the organism express thyroid hormone receptors (TR) that are mutated, and do not bond correctly with thyroid hormones, leading to some salamanders in a state of perpetual juvenile-hood. In mudpuppies, these THs are normally expressed unlike the Axolotl. However, it is believed that instead of having TH-insensitive tissues that block the effects of THs, some mudpuppy tissues, such as the external gills, have lost the ability to be regulated by TH over time. This selective insensitivity to THs suggests a normal level of activity in the hypothalamo-pituitary-thyroid axis in developing mudpuppies, unlike other salamander breeds.

The common mudpuppy also does not have a parathyroid gland. The majority of salamanders with parathyroid glands rely on them to help with hypercalcemic regulation; hypercalcemic regulation in mudpuppies is primarily done by the Pituitary gland instead. In common mudpuppies, the purpose of the absence of a parathyroid gland is poorly understood. One reason for the absence might be the lack of variability in the climate of mudpuppies, as the parathyroid glands of salamanders vary greatly depending on seasonal changes, or whether the organism hibernates.

In Necturus, external gills begin to form as a means of combating hypoxia in the egg as egg yolk is converted into metabolically active tissue. However, molecular changes in the mudpuppy during post-embryonic development primarily due to the thyroid gland prevent the internalization of the external gills as seen in most salamanders that undergo metamorphosis. The external gills seen in salamanders differs greatly from that of amphibians with internalized gills.Unlike amphibians with internalized gills which typically rely on the changing of pressures within the buccal and pharyngeal cavities to ensure diffusion of oxygen onto the gill curtain, neotenic salamanders such as Necturus use specified musculature to move external gills to keep the respiratory surfaces constantly in contact with new oxygenated water

Jacob:
Overview:

Amphibians possess two types of glands, mucous and granular (serous). Both of these glands are part of the integument and thus considered cutaneous. Mucous and granular glands are both divided into three different sections which all connect to structure the gland as a whole. The three individual parts of the gland are the duct, the intercalary region, and lastly the alveolar gland (sac). Structurally, the duct is derived via keratinocytes and passes through to the outer surface of the epidermal skin layer thus allowing external secretions of the body. The gland alveolus is the basal layer of the granular gland located in the stratum sponganium with cell layers specializing in secretion. Between the alveolar gland and the duct is the intercalary system which can be summed up as a transitional region connecting the duct to the grand alveolar beneath the epidermal skin layer. In general, granular glands are larger in size than the mucous glands, however mucous glands hold a much greater majority in overall number.

Granular Glands:

Granular glands can be identified as venomous and often differ in the type of toxin as well as the concentrations of secretions across various orders and species within the amphibians. They are located in clusters differing in concentration depending on amphibian taxa. The toxins can be fatal to most vertebrates or have no effect against others. These glands are alveolar meaning they structurally have little sacs in which venom is produced and held before it is secreted upon defensive behaviors.

Structually, the ducts of the granular gland initially maintain a cylindrical shape. However, when the ducts become mature and full of toxic fluid, the base of the ducts become swollen due to the pressure from the inside. This causes the epidermal layer to form a pit like opening on the surface of the duct in which the inner fluid will be secreted in an upwards fashion.

The intercalary region of granular glands are more developed and mature in comparison with mucous glands. This region resides as a ring of cells surrounding the basal portion of the duct which are argued to have an ectodermal muscular nature due to their influence over the lumen of the duct with dilation and constriction functions during secretions. The cells are found radially around the duct and provide a distinct attachment site for muscle fibers around the gland's body.

The gland alveolus is a sac that is divided into three specific regions/layers. The outer layer or tunica fibrosa is composed of densely packed connective-tissue which connects with fibers from the spongy intermediate layer where elastic fibers reside as well as nerves which signals to the muscles as well as the epithelial layers. Lastly, the epithelium or tunica propria encloses the gland.

(Need Images--currently consulting with non-open sources)

Mucous Glands:

Mucous glands are non-venomous and offer a different functionality for amphibians than granular. Mucous glands cover the entire surface area of the amphibian body and specialize in keeping the body lubricated. There are many other functions of the mucous glands such as controlling the pH, thermoregulation, adhesive properties to the environment, anti-predator behaviors (slimy to the grasp), chemical communication, even anti-bacterial/viral properties for protection against pathogens.

The ducts of the mucous gland appear as cylindrical vertical tubes which break through the epidermal layer to the surface of the skin. The cells lining the inside of the ducts are oriented with their longitudinal axis forming 90 degree angles surrounding the duct in a helical fashion.

Intercalary cells react identical to those of granular glands but on a smaller scale. Among the amphibians, there are taxa which contain a distinct and unique intercalary region, yet the majority share the same structure.

The alveolor of mucous glands are much more simple and only consist of an epithelium layer as well as connective tissue which forms a cover over the gland. This gland lacks a tunica propria and appears to have delicate and intricate fibers which pass over the gland's muscle and epithelial layers.

Cassidy
Edited mudpuppy page in the teeth section