Lab 2 Phyla Porifera, Cnidaria and Ctenophora.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Invertebrate Zoology Lab 2\n",
    "## Phyla Porifera,Cnidaria and Ctenophora                           \n",
    "<span style=\"color:red;\">10 September, 2021</span>\n",
    "\n",
    " \n",
    "\n",
    "---\n",
    "Today’s lab is the first in which you will learn the large-scale structure of taxonomic diversity and some morphological/structural detail of phyla we will discuss in lecture. The lab includes dissections (or looking at already dissected specimens), looking at slides and preserved and live specimens.  This lab is organized into 5 different stations each corresponding to a taxonomic group.  Work through each station at your own pace.  What you are expected to do with the organisms at each station is written out for you in detail in this handout.  **You are required to know all of the taxa and the morphological structures and larval stages that are in bold type.** Upload your required drawings into your copy of this lab using jupyter before Wednesday September 18.  \n",
    "\n",
    "* **The organisms you will see oday fall within the following taxonomic groups**\n",
    "    * <span style=\"color:red\">Phylum</span> **Porifera**\n",
    "        - <span style=\"color:blue\">Class</span> Calcarea *(small sponges)*\n",
    "            - *Grantia*\n",
    "            - *Leucoselenia*\n",
    "        - <span style=\"color:blue\">Class</span> **Desmospongea** *(most big complex sponges)*\n",
    "            - *Mirociona prolifera*\n",
    "            - *Spongilla*\n",
    "            - *Chondrosia (chicken liver sponge)*\n",
    "            - *Pseudaxinella (red ball sponge)*\n",
    "            - *Cliona*\n",
    "        - <span style=\"color:blue\">Class</span> **Hexactinellida**\n",
    "            - *Euplectella asperilligum*\n",
    "    * <span style=\"color:red\">Phylum</span> **Cnidaria**\n",
    "        - <span style=\"color:blue\">Class</span> **Hydrozoa**\n",
    "            - <span style=\"color:purple\">Order</span> **Hydroida**\n",
    "                - *Obelia*\n",
    "                - *Hydra*\n",
    "                - *Plumularia*\n",
    "            - <span style=\"color:purple\">Order</span> **Chondrophora** *(Dried up)*\n",
    "                - *Velella*\n",
    "            - <span style=\"color:purple\">Order</span> **Siphonophora**\n",
    "                - *Physalia pelagic*\n",
    "            - <span style=\"color:purple\">Order</span> Trachylina\n",
    "                - *Gonionemus*\n",
    "            - <span style=\"color:purple\">Order</span> **Milleporina** *(fire coral)*\n",
    "        - <span style=\"color:blue\">Class</span> **Scyphozoa**\n",
    "            - <span style=\"color:purple\">Order</span> Samaeostoma\n",
    "                - *Aurelia*\n",
    "            - <span style=\"color:purple\">Order</span> Rhizostomae\n",
    "                 - *Cassiopeia (the Mangrove jellyfish)*\n",
    "        - <span style=\"color:blue\">Class</span> **Anthozoa**\n",
    "            - <span style=\"color:skyblue\">Subclass</span> **Hexacorallia**\n",
    "                - <span style=\"color:purple\">Order</span> **Actinaria** *(sea anemones)*\n",
    "                    - *Metridium*\n",
    "                    - *Anthopleura*\n",
    "                - <span style=\"color:purple\">Order</span> **Scleractinia** *(true or stony corals)*\n",
    "            - <span style=\"color:skyblue\">Subclass</span> **Octocorallia**\n",
    "                - <span style=\"color:purple\">Order</span> Stolonifera *(organ pipe corals)*\n",
    "                - <span style=\"color:purple\">Order</span> Alcyonancea *(soft corals)*\n",
    "                - <span style=\"color:purple\">Order</span> **Gorgonaceae** *(sea fans and sea whips)*\n",
    "                - <span style=\"color:purple\">Order</span> **Pennatulaceae** *(sea pens and sea pansies)*\n",
    "    * <span style=\"color:red\">Phylum</span> **Ctenophora** \n",
    "\n",
    "### Objectives\n",
    " **After this lab you should:**\n",
    "1. Be able to identify specimens in the taxonomic groups above which are in bold, and be introduced to the groups not in bold\n",
    "2.  Recognize the anatomical features in bold text in this handout\n",
    "3.  Know the anatomy and life cycle of Hydra.\n",
    "4.  Know the colony structure and individual zooids of Obelia\n",
    "5.  Know the anatomy and life cycle of Aurelia.\n",
    "6.  Know the anatomy and life cycle of Metridium.\n",
    "7.  See cnidae fire and anemones eat\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Phylum Porifera sponges  \n",
    "\n",
    "Diversity: 7,000 – 15,000 species  \n",
    "Marine and freshwater  \n",
    "\n",
    "Important characteristics:\n",
    "- Asymmetrical or radially symmetrical\n",
    "- **Choanocytes**\n",
    "- **Spicules**\n",
    "- No true tissues\n",
    "- No nerve\n",
    "- Muscle cells\n",
    "\n",
    "**See slides of porifera whole mounts, spicules and chanocytes. Note that the c.s. and x.s. slides are the most clear. Be able to recognize these organisms and the following structures: spicules, choanocytes, pinacocytes (make up pinacoderm).  Drawing optional – a good idea for creating a study guide for the practicum.**\n",
    "\n",
    "\n",
    "![image1][1]\n",
    "\n",
    "[1]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image001.jpg?raw=true\n",
    "\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Phylum Cnidaria\n",
    "Diversity:  approx 11,000 extant species  \n",
    "Date from the Precambrian  \n",
    "Range in size from microscopic to jellyfish 2 meters across with tentacles 25 m long  \n",
    "\n",
    "Important characteristics:\n",
    "- **Cnidae** \n",
    "- **Mouth surrounded by tentacles**\n",
    "- **Diploblastic**\n",
    "- **Radially symmetrical**\n",
    "- **Alternation of generations**\n",
    "- **Typically have planular larvae**\n",
    "- No circulatory system\n",
    "- No CNS\n",
    "- Nerve system is simple nerve net\n",
    "- Gut (**coelenteron**) is saclike or branched, has single opening which serves as both mouth and anus.\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Class Hydrozoa  hydra, fire corals, Portuguese man o' war, wind sailor  \n",
    "Diversity:  approx 3,700 species in 7 orders  \n",
    "Includes freshwater and marine groups  \n",
    "\n",
    "Important characteristics:\n",
    "* **Alternation of generations** - asexual benthic **polyps** and sexual planktonic **medusae**\n",
    "* **Polyps usually colonial and often polymorphic**\n",
    "* **Cnidae only in epidermis**\n",
    "* Exoskeleton usually chitin or occasionally CaCO3\n",
    "* Medusa usually small, transparent and **with ring canal**\n",
    "* Mouth typically on **manubrium** "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**<u>Drawing 1 - **Hydra**</u>**  \n",
    "\n",
    "* Draw w.m. and x.s. slides, on a single page and label them as in the figure below.  Longitudinal slides may help but most of them are poor quality. \n",
    "\n",
    "* Label everything you can identify, but be sure to not miss the following:  \n",
    "\n",
    "  * **Nematocysts** \n",
    "  * **Coelenteron**\n",
    "  * **Basal (pedal) disc**\n",
    "  * Testis\n",
    "  * Ovary\n",
    "  * **Epidermis**\n",
    "  * **Mesoglea**\n",
    "  * **Gastrodermis**\n",
    "  * **Hypostome (the area around the mouth)**  \n",
    "  \n",
    "  Some of these features will not be visible on the whole mount. \n",
    "\n",
    "![image2][2]\n",
    "![Hydraxs.jpg][3]\n",
    "\n",
    "[2]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image003.jpg?raw=true\n",
    "\n",
    "[3]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/Hydraxs.jpg?raw=true"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**<u>Drawing 2 - Obelia</u>**  \n",
    "\n",
    "* Look at Obelia colony w.m. medusa and planula slides  \n",
    "* Draw and label the parts as in handout figure below  \n",
    "* Label everything you can identify, but be sure to not miss:  \n",
    "  - On **colony - gastrozooid**, \n",
    "  - **Gonozooid**\n",
    "  - **Mouth**\n",
    "  - **Hypostome**\n",
    "  - **Tentacle**\n",
    "  - **Hydrotheca**\n",
    "  - **Medusa bud**\n",
    "  - **Hydrocaulus**\n",
    "  - **Stolon \n",
    "  * on **medusa - manubrium**\n",
    "  - **Gonads**\n",
    "  - **Radial canal**\n",
    "  - **Ring canal**\n",
    "  - **Planula** \n",
    "  \n",
    "![image3][3]\n",
    "\n",
    "[3]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image005.jpg?raw=true\n",
    "\n",
    "Look at the specimens of Hydrozoa in the collection.  They are both in jars and on slides.  Try to classify each as colonial or solitary.  It is a good idea to sketch quickly representative specimens and their life cycles to study for the practical exam.\n",
    "\n",
    "Note the fire coral, **Millipora**.  This coral can be distinguished from the Anthozoan corals by the absence of septa, and the presence of two sizes of pores over the surface. The larger pores correspond to the gastrozooids and the smaller pores to the dactylozooids.  The smaller pores are often set in irregular circles around the larger pores."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### <u> Order Siphonophora </u>  \n",
    "Be sure to take a close look at the Physalia pelagica. See slide of **cross section of tentacle**."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### <u>Order Chondrophora</u>  \n",
    "*<u>Velella</u>*<u> (by the wind sailor)</u>  \n",
    "\n",
    "Unfortunately our specimens dried up, so no drawings of these are required. These are commonly found on the Oregon Coast, so I hope to get some before the semester is over.  They are extraordinarily cool in my opinion.   \n",
    "\n",
    "*Velella*  are pelagic hydrozoans that float on the surface and capture the wind with a sail to move them through the water.  *Velella* float by a combination of water-repellent mucus produced by glands around the base of the sail and air-filled float chambers.  The sail is composed of a material that has structural properties not unlike those of hyaline cartilage.  The stiffness of the material is somewhere between that of rubber and that of insect cuticle.  The sail's resistance to bending is due to the shape of the sail and the thickened ridges that reinforce it.  Oddly enough there are left-sailing and right-sailing morphs of *Velella*.  Rather than sailing downwind, *Velella* sail at an angle of up to 45 degrees to the wind, either left or right. One explanation for this strange distribution of morphs is that the counter-clockwise circulation of winds in this region tends to push the left sailing morphs closer to shore and the right sailing forms further away.  \n",
    "\n",
    "![image4][4]\n",
    "![image5][5]\n",
    "\n",
    "[4]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image007.png?raw=true\n",
    "\n",
    "[5]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image009.jpg?raw=true\n",
    "\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Class Scyphozoa  jellyfish\n",
    "\n",
    "Diversity: approx 200 species in 4 orders  \n",
    "exclusively marine  \n",
    "\n",
    "Important characteristics:\n",
    "* **Medusoid stage predominates**\n",
    "* Polyps produce medusa by asexual budding (**strobilation**)\n",
    "* **Coelenteron divided by longitudinal septa**, medusa lacks a velum, typically has a **thick mesogleal layer**, distinct pigmentation\n",
    "* Sense organs occur in notches alternating with tentacles\n",
    "* Cnidae present in epidermis and gastrodermis\n",
    "* Usually **without a ring canal**"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**<u>Drawing 3 - Aurelia.</u>**  \n",
    "- *Aurelia* lives in coastal waters and feeds on plankton.  It often occurs in great numbers close to shore and thus is easy to collect for invertebrate zoology classes.   \n",
    "\n",
    "- Immerse a specimen of the moon jellyfish, *Aurelia*, in water in a blue dissecting tray or a watch glass. Most of the characteristics to see are visible without magnification, but you can also look at them under the dissecting scope. \n",
    "\n",
    "- Find the parts labeled in the figure below and draw and label the parts of an oral view of the specimen.  Label everything you can identiify, but be sure to label the following:  mouth, oral arm, tentacles, rhopalium, gonad.  Make sure the specimen is completely immersed and add a drop of methylene blue to improve the contrast.  You might try placing the drop in the oral cavity and watching where it diffuses.  \n",
    "\n",
    "- Notice *Aurelia* lacks a velum.  In medusa that have a velum it serves to decrease the size of the opening where water is forced out, thus increasing the propulsive force.  Would you expect *Aurelia*  capable of speedy evasive maneuvers? \n",
    "\n",
    "- How does *Aurelia* eat?  Swimming and eating are inseparable for this creature because it feeds by filtering plankton from the water with its fringe of tentacles or trapping them in mucus secreted on its subumbrellar surface.  The oral arms then sweep the trapped plankton off the margins and into the mouth.  \n",
    "\n",
    "![image6][6]\n",
    "\n",
    "[6]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image011.png?raw=true\n",
    "\n",
    "- Swimming is accomplished by contraction of muscle fibers that cause the bell to contract and force water out.  How does the bell contract?  *Aurelia* has eight pacemaker ganglia that are each able to generate an impulse that contracts the bell.  When all ganglia are intact, the bell contracts in a rhythmic fashion in stable cycles.  When one ganglion generates an impulse it causes the whole bell to contract and resets all the other ganglia so they can't fire for a refractory period.  If you remove all the ganglia except one, the medusa can still swim but the pattern of contractions becomes irregular.  Where do you think the ganglia are located? How does the bell expand?  The mesoglea of *Aurelia* is composed of a protein and polysaccharide matrix that is slightly less dense than sea water and serves two major swimming functions.  First, it gives the medusa a bit of buoyancy.  Secondly, its resilience causes the bell to reform its pre contraction shape after relaxation of the muscle fibers.  The expansion of the bell is much slower than the contraction, helping the medusa to swim in an aboral direction. \n",
    "\n",
    "- What is the function of the radial and ring canals and how do they work?  If fluid is circulated in them, what is the pattern of circulation and where does fluid enter and exit the system?\n",
    "\n",
    "**Life cycle of *Aurelia***  \n",
    "Look at the developmental slides of *Aurelia* **planula**, **scyphistoma** and **ephyra**. **Sketch these on your *Aurelia*.  Look at other specimens of scyphozoans in the collection.**  It is a good idea to sketch quickly these to study for the practical exam.\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Class Anthozoa sea anemones, corals, sea pens\n",
    "\n",
    "Diversity:  6,000 sp in 3 subclasses (~70% of all Cnidarians)\n",
    "exclusively marine  \n",
    "\n",
    "Important characteristics:  \n",
    "* Solitary or colonial\n",
    "* **Without medusoid stage**\n",
    "* **Cnidae epidermal and gastrodermal**\n",
    "* Divided by **longitudinal mesentaries**\n",
    "* Mesenchyme thick\n",
    "* Tentacles - 8 or multiples of 6 and contain extensions of the coelenteron\n",
    "* Have **siphonoglyph**\n",
    "* Polyps reproduce sexually and asexually  \n",
    "\n",
    "**Subclass Octocorallia** (8 mesenteries) sea fans, sea pansies, soft corals  \n",
    "**Subclass Hexacorallia** (mesentaries in multiples of 6) sea anemones, true corals"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**<u>Drawing 4 - Metridium.</u>**  \n",
    "\n",
    "* Dissect, draw and label a *Metridium* specimen as in the figure below.  First make a longitudinal cut through one wall and then spread the two ends to view and draw the internal anatomy.  When this is complete, make a cross section and determine the relative position the cut is to the pharynx and draw the internal anatomy.  Label everything you can identify but be sure to look for the following:  \n",
    "    * **Oral disc**\n",
    "    * **Mouth**\n",
    "    * **Siphonoglyph**\n",
    "    * **Mesenterial filaments**\n",
    "    * **Gonads**\n",
    "    * **Pedal disc**\n",
    "    * Cross section\n",
    "      - **Pharynx**\n",
    "      - **Epidermis**\n",
    "      - **Mesenchyme**\n",
    "      - **Gastrodermis**\n",
    "      - **Coelenteron**\n",
    "      - **Retractor muscles**\n",
    "      \n",
    "\n",
    "* *Metridium* movement—The handout figure below shows the range of shapes *Metridium* can adopt. *Metridium* can deform its shape by contracting the longitudinal, circular and radial retractor muscles or inflating itself by pumping water into the gastrovascular cavity through the siphonoglyph.  If the *Metridium* closes its mouth and inflates itself with the siphonoglyph, in about an hour it will look like it will be rounded, and if the circular muscles are contracted when the longitudinal muscles are contracted it will be elongate and narrow.  If disturbed, *Metridium* can protect its tentacles or completely retract .  \n",
    "\n",
    "\n",
    "* The properties of *Metridium* mesoglea in conjunction with the musculature allow the animal to assume these shapes.  *Metridium&  mesoglea is composed of a collagenous protein loosely imbedded in a matrix of polysaccharides and is a viscoelastic fluid.  It can be stretched up to three times its initial length but returns to its original shape when unstressed.  It resists deforming under brief forces (like waves) yet deforms under a small constant force acting over a longer period of time (like the pumping action of the siphonoglyph).  This is why something as feeble as the pumping of water into the gastrovascular cavity with flagella can serve to inflate *Metridium*.\n",
    "\n",
    "![image7][7]\n",
    "![image8][8]\n",
    "\n",
    "[7]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image013.png?raw=true\n",
    "[8]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image015.jpg?raw=true\n",
    "\n",
    "**Observe preserved anemones in various stages of retraction.**  Later in the course we will have the opportunity to watch movement in live anemones.  \n",
    "\n",
    "**Look at the specimens of the class Anthozoa in the invertebrate collection.**  It is a good idea to quickly sketch representative members of this group and their life cycles to study for the practical exam.   \n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Phylum Ctenophora comb jellies, sea gooseberries, sea walnuts\n",
    "Diversity:  ~ 200 species described in two classes. \n",
    "\n",
    "Important characteristics:  \n",
    "* **Diploblastic (or tiploblastic)** with ectoderm and endoderm separated by a cellular mesenchyme\n",
    "* **Biradial symmetry**\n",
    "* **Colloblasts** (adhesive structures)\n",
    "* Gut with stomodeum and canals that branch complexly throughout body\n",
    "* Gut ends in two small anal pores\n",
    "* No gas exchange, excretory or circulatory systems\n",
    "* Nervous system in form of nerve net or nerve plexus\n",
    "* Monomorphic\n",
    "* **8 rows of ciliary plates** at some life stage\n",
    "* Most hermaphroditic.\n",
    "\n",
    "**No drawing – be sure to see images of these and we’ll try to get better specimens. Recognize images as ctenophores. See  & recognize the comb rows (= cilliary plates)!** \n",
    " \n",
    " \n",
    "![image9][9]\n",
    "\n",
    "[9]: https://github.com/watzek/Invertebrate-Labs/blob/master/images/lab2/image017.jpg?raw=true\n",
    " \n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Upload image files for the drawings you did, and any other supplemental photos you want into your personal jupyter version of this document. Complete this before Wednesday 5 pm Sept 18.** "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## How to add images to your jupyter noteboook:\n",
    "\n",
    "#### First navigate to the correct folder\n",
    "\n",
    "- In your home directory in Jupyter Notebooks (get there by clicking the Jupyter logo), you should have a folder titled 'bio317'. Inside that folder, you'll have a folder called 'images'. And inside images, you'll have a number of folders corresponding to each lab (e.g. lab2, lab3, etc.).\n",
    "- Navigate to the folder corresponding to the lab you're doing (e.g., if you're working on lab2, navigate to 'bio317/images/lab2').\n",
    "\n",
    "\n",
    "#### Loading and referencing images\n",
    "- Once you're in the correct folder, click the 'Upload' button, and then choose a file from your computer.\n",
    "- At this point you can optionally rename the image. Make sure you click \"Upload\" again. **Pro tip: DO NOT include spaces in your file name. Use underscores instead**\n",
    "- Now construct the URL of your image. The syntax for all images is:  \n",
    "\n",
    "`https://datasci.watzek.cloud/shared/bio317/<your username>/images/<lab folder>/<filename>`\n",
    "\n",
    "Making mistakes here is pretty easy. Probably the best approach is to copy the example syntax above, and then fill in the blanks.\n",
    "\n",
    "For example, say your username is 'fred', you're working on lab 2, and your image is called 'myImage.jpg'. Your image URL would be:  \n",
    "\n",
    "`https://datasci.watzek.cloud/shared/bio317/fred/images/lab2/myImage.jpg`\n",
    "\n",
    "\n",
    "\n",
    "- Now in your notebook, double-click the cell to edit.\n",
    "- Enter the following syntax, where `alt text` is the text that appears for screen readers, the full URL is the path to the image, and `hover text` is the text that appears when you hover your mouse over the image:\n",
    "\n",
    "`![alt text](https://datasci.watzek.cloud/shared/bio317/jeremym/images/lab2/my_dog.jpg \"hover text\")`\n",
    "\n",
    "The result is below:\n",
    "\n",
    "![alt text](https://datasci.watzek.cloud/shared/bio317/jeremym/images/lab2/my_dog.jpg \"hover text\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}