<p class="jove_content">The authors acknowledge with gratitude the skillful assistance of Mrs. Trine W. Mikkelsen, Mrs. Lise M. Fitting, and the staff at P&#229;skeh&#248;jgaard. The Danish Medical Research Council, the Lundbeck Foundation, and the Novo Nordisk Foundation financially supported the study.</p>

<p class="jove_content">Animal anesthesia and euthanesia was performed in accordance with &#34;Principles of laboratory animal care&#34; (NIH publication No. 86-23, revised 1985) and approved by the Danish Council for Animal Research Ethics.</p>
<p class="jove_title">1. Instruments</p>
<ol>
	<li>Collect the instruments presented in the video and listed in the <strong>Table of Materials</strong>.</li>
</ol>
<p class="jove_title">2. Decapitation</p>
<p class="jove_content">NOTE: Anesthesia was induced by an intramuscular injection of 5 mL of midazolam (5 mg/mL) and 5 mL of ketamine (25 mg/mL). 5-10 min later, when the animal was deeply sedated, an ear vein was cannulated and a lethal overdose (100 mg/kg of bodyweight) of sodium pentobarbital (200 mg/mL) was given intravenously. To ensure that the animal was completely euthanized, the interdigital pain reflex was tested as shown by Ettrup <em>et al.</em> (2011)<sup class="xref">20</sup>. Complete euthanization was ensured as described in the ethics statement above and followed by a transcardial perfusion with 5 L of isotonic saline, as demonstrated by Ettrup <em>et al. </em>(2011)<sup class="xref">20</sup>. All the demonstrated procedures are performed postmortem, precluding the need for the welfare precautions necessary for long-term anesthesia and postprocedural survival.</p>
<ol>
	<li>Decapitate the pig by a high circular cervical incision, using a surgical scalpel, just below the mandibular angle (<strong>Figure 1A</strong>).</li>
	<li>Still with the surgical scalpel, continue the incision anteriorly through the soft tissue of the neck, including the larynx and the esophagus, until the bony spinal column is reached, approximately at the level of the craniocervical junction.</li>
	<li>Advance the cut with a surgical scalpel from the anterior side of the craniocervical junction, above the anterior arc of atlas, and through the anterior atlantooccipital membrane, thereby exposing the spinal canal and the spinal cord (<strong>Figure 1B</strong>). Simultaneously ask an assistant to pull the pig body away from the pig head to ease the access between the skull base and the first cervical vertebra.</li>
	<li>Continue the surgical incision through the dural sac and the spinal cord (<strong>Figure 1B</strong>). Take special care to ensure that a complete transverse section of the spinal cord is achieved.<br />
	NOTE: Failure to perform the previous step may result in unwanted traction on the spinal cord and brain during the following steps of the decapitation process.</li>
	<li>Forcefully extend the cranocervical junction at the section level (<strong>Figure 1C</strong>). At the same time, use the surgical scalpel to section the remaining atlantooccipital ligaments to release the articulation between the occipital condyles and the upper articulate process of atlas. Separate the pig head from the body.</li>
</ol>
<p><img alt="Figure 1" src="/files/ftp_upload/55511/55511fig1.jpg" style="font-size: 14px;" /><br style="font-size: 14px;" />
<strong style="font-size: 14px;">Figure 1: Minipig decapitation.</strong>&#160;(<strong>A</strong>) Neck incision (arrow, mandibular angle). (<strong>B</strong>) Incision through the atlantooccipital ligaments and the dura-surrounded spinal cord (SC) at the craniocervical junction (C1, anterior arc of atlas; OC, occipital condyle). (<strong>C</strong>) The posterior part of the atlantooccipital articulation is released by a forceful extension (arrows) at the section level.&#160;<a href="http://cloudfront.jove.com/files/ftp_upload/55511/55511fig1large.jpg" style="font-size: 14px;" target="_blank">Please click here to view a larger version of this figure.</a></p>
<p class="jove_title">3. Skull Opening</p>
<ol>
	<li>Position the pig head on a table.</li>
	<li>Make a dorsal longitudinal incision with a surgical scalpel through the skin and the underlying soft tissue from the back of the snout, over the vertex of the head, and down through the posterior part of the occipital region.</li>
	<li>Expose the dorsal and posterior part of the skull by removing the soft tissue located lateral to the initial incision with a surgical scalpel.</li>
	<li>Release the temporal muscle bilaterally from the skull (<strong>Figure 2A</strong>) with a surgical scalpel. Make sure that the posterior occipital bone is cleaned of soft tissue.</li>
	<li>Use the posterior entrance of the foramen magnum to remove the occipital bone with a Kerrison bone punch and bone rongeurs and expose the dura-covered cerebellum (<strong>Figure 2B</strong>).</li>
	<li>Return to the exposed anterior side of the skull and select an entry point in the frontal bone, just in front of the eyes. At this point, use a bone chisel with a hammer to penetrate the skull and enter the frontal sinus (<strong>Figure 2C</strong>).</li>
	<li>Use the extent of the frontal sinus to further the dorsoposterior removal of the outer skull lamina with a bone rongeur or bone punch and expose the inner, thin bony skull lamina covering the cerebrum (<strong>Figure 2D</strong>).</li>
	<li>Gently open the inner bony skull lamina anteriorly with a hammer and a bone chisel to expose the dura-covered cerebrum (<strong>Figure 2E</strong>).</li>
	<li>Continue the bone removal laterally using a bone chisel and a bone rongeur through the temporal and parietal bone in order to release the final dorsoposterior part of the skull, located between the already exposed parts of the dura-covered cerebrum and cerebellum (<strong>Figure 2F</strong>).<br />
	NOTE: It is often possible, during the final step of this procedure, to use the chisel to break open the remaining posterior skull bone from one side, just like one opens a door.</li>
</ol>
<p><img alt="Figure 2" src="/files/ftp_upload/55511/55511fig2.jpg" style="opacity: 0.9; font-size: 14px;" /><br style="font-size: 14px;" />
<strong style="font-size: 14px;">Figure 2: Minipig skull opening.</strong>&#160;(<strong>A</strong>) Exposure of the dorsoposterior skull surface, including the removal of the occipital and temporal muscles. (<strong>B</strong>) Removal of the occipital bone (CB, dura-covered cerebellum; OB, occipital bone; OC, occipital condyle; and SC, spinal cord). (<strong>C</strong>) A hammer and a bone chisel are used to penetrate the skull anteriorly and to enter the frontal sinus at the level of the eyes. (<strong>D</strong>) The extent of the frontal sinus (FS) is used to remove the outer thick skull bone (1), exposing an inner thin bone lamina (2) covering the cerebrum. (<strong>E</strong>) Removal of the thin bone lamina, exposing the dura-covered cerebrum (arrow). (<strong>F</strong>) Finally, a hammer and a bone chisel are used to laterally connect the anterior and the posterior skull openings.&#160;<a href="http://cloudfront.jove.com/files/ftp_upload/55511/55511fig2large.jpg" style="font-size: 14px;" target="_blank">Please click here to view a larger version of this figure.</a></p>
<p class="jove_title">4. Brain Removal</p>
<ol>
	<li>Use surgical forceps to lift the dura and create a gentle incision close to the venous superior sagittal sinus using a fine surgical scalpel (<strong>Figure 3A</strong>).</li>
	<li>Use micro-scissor or a dura-knife to further open the dura covering the dorsal surface of the brain.<br />
	NOTE: Special care must be taken when removing the dura corresponding to the cerebellar tentorium (Figure 3B), as preservation of this dural leaf will prevent subsequent brain removal.</li>
	<li>Position the pig head vertically (<strong>Figure 3C</strong>).</li>
	<li>Use the bone chisel or a dissector to release the ventroanterior cerebrum by blunt dissection of the olfactory bulb from the dura-covered floor of the cranial cavity (<strong>Figure 3D</strong>).</li>
	<li>Use a fine surgical scalpel to section the exposed optic chiasm (<strong>Figure 3E</strong>). Expose and section the pituitary stalk and the oculomotor nerves.</li>
	<li>Release the ventral brainstem by sectioning the lower cranial nerves (<strong>Figure 3F</strong>) with a fine surgical scalpel. Ensure that the dural cerebellar tentorium was completely incised (<strong>Figure 3B</strong>), as this dural leaf will otherwise cut through the brainstem during the release process.</li>
</ol>
<p><img alt="Figure 3" src="/files/ftp_upload/55511/55511fig3.jpg" style="font-size: 14px;" /><br style="font-size: 14px;" />
<strong style="font-size: 14px;">Figure 3: Minipig brain removal.</strong>&#160;(<strong>A</strong>) Dural opening with surgical forceps and a dura knife. (<strong>B</strong>) Care must be taken to completely incise the dural leaf (arrow), located between the cerebrum and the cerebellum. (<strong>C</strong>) The pig head is positioned vertically for better visualization of skull base structures and in order for gravity to assist in the intended displacement of the brain. (<strong>D</strong>) A dissector or a bone chisel is used to relieve the olfactory bulb by blunt section from the dura-covered skull base. (<strong>E</strong>) The dissection is continued in a posterior direction along the skull base for exposure and sectioning of the optic chiasm (arrow), infundibular stalk, and oculomotor nerves. (<strong>F</strong>) The brain release is completed with the section of the lower cranial nerves as they depart from the ventral surface of the brainstem (III, oculomotor nerve; IV, trochlear nerve; V, trigeminal nerve; and VI, abducens nerve).&#160;<a href="http://cloudfront.jove.com/files/ftp_upload/55511/55511fig3large.jpg" style="font-size: 14px;" target="_blank">Please click here to view a larger version of this figure.</a></p>
<p class="jove_title">5. Pituitary Removal</p>
<ol>
	<li>Identify the pituitary stalk and its surrounding dural leaf (the diapragma sellae) in the skull floor (<strong>Figure 4A</strong>).</li>
	<li>Incise the dural leaf lateral to the pituitary stalk using a fine surgical scalpel (<strong>Figure 4B</strong>).</li>
	<li>Use a dissector to release the pituitary and lift it out of the pituitary fossa (<strong>Figure 4C</strong>).</li>
</ol>
<p><img alt="Figure 4" src="/files/ftp_upload/55511/55511fig4.jpg" style="opacity: 0.9; font-size: 14px;" /><br style="font-size: 14px;" />
<strong style="font-size: 14px;">Figure 4:</strong>&#160;Minipig pituitary removal. (<strong>A</strong>) The pituitary fossa (*) is identified in the skull floor (1, olfactory bulb; 2, optic chiasm; and PF, posterior cranial fossa). (<strong>B</strong>) The dural covering (sellar diagphragm, (arrow)) is incised laterally. (<strong>C</strong>) The pituitary (arrow) is released with a dissector and lifted out of the pituitary fossa. Scale bar (A-C) = 10 mm.&#160;<a href="http://cloudfront.jove.com/files/ftp_upload/55511/55511fig4large.jpg" style="font-size: 14px;" target="_blank">Please click here to view a larger version of this figure.</a></p>

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R., Gjedde, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kinetics+of+the+uptake+and+distribution+of+the+dopamine+D2/3+agonist+(R)-N-[1-11C]n-propylnorapomorphine+in+brain+of+healthy+and+MPTP-poisoned+Gottingen+miniature+pigs.">Kinetics of the uptake and distribution of the dopamine D2/3 agonist (R)-N-[1-11C]n-propylnorapomorphine in brain of healthy and MPTP-poisoned Gottingen miniature pigs.</a> <em style='font-style: italic'>Nucl Med Biol</em>. <b>30</b> (5), 547-553 (2003).</li><li>Jensen, K. N., Deding, D., S&#248;rensen, J. C., Bjarkam, C. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+substantia+nigra+pars+compacta+of+the+minipig:+An+anatomical+and+stereological+study.">The substantia nigra pars compacta of the minipig: An anatomical and stereological study.</a> <em style='font-style: italic'>Brain Struct Funct</em>.  (4-5), 481-488 (2009).</li><li>S&#248;rensen, J. C., Bjarkam, C. R., Simonsen, C. Z., Danielsen, E., Geneser, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oriented+sectioning+of+irregular+tissue+blocks+in+relation+to+computerized+scanning+modalities.+Results+from+the+domestic+pig+brain.">Oriented sectioning of irregular tissue blocks in relation to computerized scanning modalities. Results from the domestic pig brain.</a> <em style='font-style: italic'>J Neurosci Methods</em>. <b>104</b>, 93-98 (2000).</li><li>Bjarkam, C. R., Pedersen, M., S&#248;rensen, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+strategies+for+embedding,+orientation+and+sectioning+of+small+brain+specimens+enable+direct+correlation+to+MR-images,+brain+atlases,+or+use+of+unbiased+stereology.">New strategies for embedding, orientation and sectioning of small brain specimens enable direct correlation to MR-images, brain atlases, or use of unbiased stereology.</a> <em style='font-style: italic'>J Neurosci Methods</em>. <b>108</b>, 153-159 (2001).</li><li>Bjarkam, C. R., S&#248;rensen, J. C., Geneser, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distribution+and+morphology+of+serotonin-immunoreactive+axons+in+the+hippocampal+region+of+the+New+Zealand+white+rabbit.+I.+Area+dentata+and+hippocampus+proper.">Distribution and morphology of serotonin-immunoreactive axons in the hippocampal region of the New Zealand white rabbit. I. Area dentata and hippocampus proper.</a> <em style='font-style: italic'>Hippocampus</em>. <b>13</b> (1), 21-37 (2003).</li><li>Bjarkam, C. R., Glud, A. N., Orlowski, D., S&#248;rensen, J. C., Palomero-Gallagher, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+telencephalon+of+the+minipig,+cytoarchitecture+and+cortical+surface+anatomy.">The telencephalon of the minipig, cytoarchitecture and cortical surface anatomy.</a> <em style='font-style: italic'>Brain Struct Funct</em>. , (2016).</li><li>Boltze, J., Nitzsche, B., Geiger, K. D., Schoon, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histopathological+investigation+of+different+MCAO+modalities+and+impact+of+autologous+bone+marrow+mononuclear+cell+administration+in+an+ovine+stroke+model.">Histopathological investigation of different MCAO modalities and impact of autologous bone marrow mononuclear cell administration in an ovine stroke model.</a> <em style='font-style: italic'>Transl Stroke Res</em>. <b>2</b>, 279-293 (2011).</li><li>Jortner, B. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+return+of+the+dark+neuron.+A+histological+artifact+complicating+contemporary+neurotoxicologic+evaluation.">The return of the dark neuron. A histological artifact complicating contemporary neurotoxicologic evaluation.</a> <em style='font-style: italic'>Neurotoxicology</em>. <b>27</b>, 628-634 (2006).</li></ol>

<p class="jove_content">The authors have nothing to disclose.</p>

<p class="jove_content">Most experimental neuroscience studies are performed in small animal species, such as mice and rats, where access to the CNS is facilitated by a thin skull- and dural-thickness. However, in larger experimental animals like pigs<sup class="xref">1</sup><sup>,</sup><sup class="xref">4</sup><sup>,</sup><sup class="xref">8</sup>, sheep<sup class="xref">32</sup>, and non-human primates, the considerable thickness of these structures necessitates the use of robust instruments (table of materials) and proper entry points for sk...

<p class="jove_content">Translational neuroscience studies in pigs have become increasingly popular during the last two decades. The large size of the pig brain enables the use of conventional clinical brain imagers and the direct use and testing of neurosurgical procedures and equipment from the human clinic<sup class="xref">1</sup><sup>,</sup><sup class="xref">2</sup><sup>,</sup><sup class="xref">3</sup><sup>,</sup><sup class="xref">4</sup><sup>,</sup><sup class="xref">5</sup><sup>,</sup><sup class="xref">6</sup><sup>,</sup><sup class="xref">7</sup><sup>,</sup><sup class="xref">8</sup>. In the last 20 years, pigs, especially minipigs (<em>e.g.,</em> G&#246;ttingen minipig), have been used to examine neuromodulatory treatment modalities, such as stem cell transplantation; viral vector transfection; and deep brain stimulation directed towards Parkinson disease, obesity, depression, and Alzheimer disease<sup class="xref">2</sup><sup>,</sup><sup class="xref">6</sup><sup>,</sup><sup class="xref">9</sup><sup>,</sup><sup class="xref">10</sup><sup>,</sup><sup class="xref">11</sup><sup>,</sup><sup class="xref">12</sup><sup>,</sup><sup class="xref">13</sup><sup>,</sup><sup class="xref">14</sup><sup>,</sup><sup class="xref">15</sup><sup>,</sup><sup class="xref">16</sup><sup>,</sup><sup class="xref">17</sup>. This has been followed by the development of stereotaxic and surgical approaches to manipulate the minipig CNS<sup class="xref">3</sup><sup>,</sup><sup class="xref">18</sup><sup>,</sup><sup class="xref">19</sup><sup>,</sup><sup class="xref">20</sup><sup>,</sup><sup class="xref">21</sup>. The instituted CNS changes have been evaluated in live animals using brain imaging (PET<sup class="xref">10</sup><sup>,</sup><sup class="xref">13</sup><sup>,</sup><sup class="xref">22</sup><sup>,</sup><sup class="xref">24</sup> and MR<sup class="xref">23</sup>), cystometry<sup class="xref">11</sup><sup>,</sup><sup class="xref">12</sup><sup>,</sup><sup class="xref">25</sup>, gait analysis<sup class="xref">17</sup>, neurological evaluation<sup class="xref">9</sup><sup>,</sup><sup class="xref">17</sup>, and postmortem examination based on histology and stereological analysis<sup class="xref">14</sup><sup>,</sup><sup class="xref">15</sup><sup>,</sup><sup class="xref">17</sup><sup>,</sup><sup class="xref">26</sup><sup>,</sup><sup class="xref">27</sup><sup>,</sup><sup class="xref">31</sup>. However, postmortem analysis requires the exposure and removal of the pig brain, which is not an easy task, as a thick, bony skull and a fibrous dural covering surround the pig brain.</p>
<p class="jove_content">The goal of this paper and instructional video is to describe how the postmortem pig brain and pituitary may be exposed and removed in an intact state in 15-20 min using non-motorized surgical tools. The instructional video and photographic illustrations show male minipigs (age: 6 months, bodyweight: 20-25 kg) used for an anatomical study on the minipig pituitary gland.</p>

<table><tbody><tr><td>Heavy Scalpel Handle #4</td><td>FST (Fine Science Tools)</td><td>10008-13</td><td>Good for skin incision and soft tissue removal</td></tr><tr><td>Non-Sterile Scalpel Blades #23</td><td>FST&amp;nbsp;</td><td>10023-00</td><td></td></tr><tr><td>Scalpel Handle #7</td><td>FST&amp;nbsp;</td><td>10007-12</td><td>Optimal for dural incision and precision work</td></tr><tr><td>Non-Sterile Scalpel Blades #11</td><td>FST&amp;nbsp;</td><td>10011-00</td><td></td></tr><tr><td>Surgical Forceps</td><td>FST&amp;nbsp;</td><td>11024-18</td><td>The tip of the surgical forceps ensure a firm grip&amp;nbsp;</td></tr><tr><td>Kerrison Bone Punch</td><td>Aesculap Neurosurgery</td><td>FF713R</td><td>Must be robust, bite size 3-5 mm</td></tr><tr><td>Bone Rongeur</td><td>Aesculap Neurosurgery</td><td>MD615</td><td>Must be robust, bite size 15 x 5 mm</td></tr><tr><td>Bone Rongeur</td><td>Aesculap Neurosurgery</td><td>FO551R</td><td>Must be robust, bite size 25 x 15 mm&amp;nbsp;</td></tr><tr><td>Bone Chisel</td><td>Lawton</td><td>67-0335</td><td>The size of the chisel head should not exceed 20 mm</td></tr><tr><td>Mallet (Hammer)</td><td>Millarco</td><td>5624108</td><td>Weigth 300 g, length 30 cm, head hit area size 2 x 2 cm</td></tr><tr><td>Micro-Scissor</td><td>FST&amp;nbsp;</td><td>14002-14&amp;nbsp;&amp;nbsp;</td><td></td></tr><tr><td>Dissector</td><td>Aesculap Neurosurgery</td><td>OL165R</td><td></td></tr><tr><td>G&amp;ouml;ttingen minipigs</td><td>Ellegaard G&amp;ouml;ttingen Minipigs A/S, Denmark</td><td></td><td></td></tr><tr><td>Euthanimal</td><td></td><td></td><td>pentobarbital</td></tr><tr><td>Ketamine</td><td>Pfizer</td><td></td><td></td></tr><tr><td>Midazolam&amp;nbsp;</td><td>Hameln Pharmaceuticals</td><td></td><td></td></tr></tbody></table>

exposure of the pig cns for histological analysis: a manual for decapitation, skull opening, and brain removal

<p class="jove_content">Pigs have become increasingly popular in large-animal translational neuroscience research as an economically and ethically feasible substitute to non-human primates. The large brain size of the pig allows the use of conventional clinical brain imagers and the direct use and testing of neurosurgical procedures and equipment from the human clinic. Further macroscopic and histological analysis, however, requires postmortem exposure of the pig central nervous system (CNS) and subsequent brain removal. This is not an easy task, as the pig CNS is encapsulated by a thick, bony skull and spinal column. The goal of this paper and instructional video is to describe how to expose and remove the postmortem pig brain and the pituitary gland in an intact state, suitable for subsequent macroscopic and histological analysis.</p>

<p class="jove_content" fo:keep-together.within-page="1">To prevent the tissue material from drying out, it is recommended to store the removed brain and pituitary in a jar filled with fixative or isotonic saline immediately after macroscopic analysis has been performed. The tissue material may be stored in the fixative for years, whereas storage in isotonic saline, even in a refrigerator, will lead to tissue decay with time.</p>
<p class="jove_content" fo:keep-together.within-page="1">The removed pituitary may also be directly frozen by immers...

Watch this Scientific Journal Video about Exposure of the Pig CNS for Histological Analysis: A Manual for Decapitation, Skull Opening, and Brain Removal at JoVE.com

Exposure of the Pig CNS for Histological Analysis: A Manual for Decapitation, Skull Opening, and Brain Removal

<p class="jove_content">The goal of this paper and instructional video is to describe how to expose and remove the postmortem pig brain and pituitary gland in an intact state, suitable for subsequent macroscopic and histological analysis.</p>

Pigs have become increasingly popular in large-animal translational neuroscience research as an economically and ethically feasible substitute to ...

exposure-pig-cns-for-histological-analysis-manual-for-decapitation

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Anatomy and Physiology

Neuroscience

Unit 1

The Axial Skeleton

SCIENTISTS IN ACTION

15.4K Views.  Aalborg University Hospital. The goal of this paper and instructional video is to describe how to expose and remove the postmortem pig brain and pituitary gland in an intact state, suitable for subsequent macroscopic and histological analysis.

Video: Exposure of the Pig CNS for Histological Analysis: A Manual for Decapitation, Skull Opening, and Brain Removal

Cellular Respiration

<h4>Autotrophs and Heterotrophs</h4>

<p>Living organisms require a continuous input of energy to maintain cellular and organismal functions such as growth, repair, movement, defense, and reproduction. Cells can only use chemical energy to fuel their functions, therefore they need to harvest energy from chemical bonds of biomolecules, such as sugars and lipids. Autotrophic organisms, namely plants, algae, and photosynthetic and chemosynthetic bacteria, convert inorganic materials into such biomolecules by harnessing energy from the environment, such as from sunlight during photosynthesis. Heterotrophic organisms are unable to synthesize high-energy biomolecules from inorganic materials, so they obtain energy by consuming carbon compounds produced by other organisms, primarily from autotrophs. When energy is needed, chemical bonds of carbon compounds are broken to harvest the energy stored in these bonds. The processes to harvest energy from biomolecules are called cellular respiration.</p>

<p>Cellular respiration occurs in both autotrophic and heterotrophic organisms, where energy becomes available to the organism most commonly through the conversion of adenosine diphosphate (ADP) to adenosine triphosphate (ATP). There are two main types of cellular respiration&#8212;aerobic respiration and anaerobic respiration. Aerobic respiration is a specific type of cellular respiration, in which oxygen (O<sub>2</sub>) is required to create ATP. In this case, glucose (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) can be oxidized completely in a series of enzymatic reactions to produce carbon dioxide (CO<sub>2</sub>) and water (H<sub>2</sub>O).</p>

<h4>Aerobic Respiration</h4>

<p>Aerobic respiration occurs in three stages. A process called glycolysis splits glucose into two three-carbon molecules called pyruvate. This process releases energy, some of which is transferred to ATP. Next, pyruvate molecules enter the mitochondria to take part in a series of reactions called the Krebs cycle, also known as the citric acid cycle. This completes the breakdown of glucose, harvesting some of the energy into ATP and transferring electrons onto carrier molecules. In the last stage, known as oxidative phosphorylation, electrons pass through an electron transport system in the mitochondrial inner membrane, which maintains a gradient of hydrogen ions. Cells harness the energy of this proton gradient to generate the majority of the ATP during aerobic respiration.</p>

<h4>Anaerobic Respiration</h4>

<p>Aerobic respiration requires oxygen, however, there are many organisms that live in places where oxygen is not readily available or where other chemicals overwhelm the environment. Extremophiles are bacteria that can live in places such as deep ocean hydrothermal vents or underwater caves. Rather than using oxygen to undergo cellular respiration, these organisms use inorganic acceptors such as nitrate or sulfur, which are more easily obtainable in these harsh environments. This process is called anaerobic respiration.</p>

<p>When oxygen is not present and cellular respiration cannot take place, a special anaerobic respiration called fermentation occurs. Fermentation starts with glycolysis to capture some of the energy stored in glucose into ATP. However, since oxidative phosphorylation does not occur, fermentation produces fewer ATP molecules than aerobic respiration. In humans, fermentation occurs in red blood cells that lack mitochondria, as well in muscles during strenuous activity generating lactic acid as a byproduct, therefore it is named lactic acid fermentation. Some bacteria carry out lactic acid fermentation and are used to make products such as yogurt. In yeast, a process known as alcoholic fermentation generates ethanol and carbon dioxide as byproducts, and has been used by humans to ferment beverages or leaven dough.</p>

<h4>Photosynthesis</h4>

<p>Cellular respiration together with photosynthesis is a feature of the transfer of energy and matter, and highlights the interaction of organisms with their environment and other organisms in the community. Cellular respiration takes place inside individual cells, however, at the scale of ecosystems, the exchange of oxygen and carbon dioxide through photosynthesis and cellular respiration affects atmospheric oxygen and carbon dioxide levels.</p>

<p>Interestingly, the processes of cellular respiration and photosynthesis are directly opposite of one another, where the products of one reaction are the reactants of the other. Photosynthesis produces the glucose that is used in cellular respiration to make ATP. This glucose is then converted back into CO<sub>2</sub> during respiration, which is a reactant used in photosynthesis. More specifically, photosynthesis constructs one glucose molecule from six CO<sub>2</sub> and six H<sub>2</sub>O molecules by capturing energy from sunlight and releases six O<sub>2</sub> molecules as a byproduct. Cellular respiration uses six O<sub>2</sub> molecules to convert one glucose molecule into six CO<sub>2</sub> and six H<sub>2</sub>O molecules while harnessing energy as ATP and heat.</p>

<h4>Measuring Respiration</h4>

<p>Scientists can measure the rate of cellular respiration using a respirometer by assessing the rate of exchange of oxygen. Understanding the Ideal Gas Law is of fundamental importance for knowing how the respirometer functions. The Ideal Gas Law states that the number of gas molecules in a container can be determined from the pressure, volume, and temperature. More specifically, the product of the volume and pressure of a gas equals the product of the number of gas molecules, the ideal gas constant and the temperature of the gas. Respirometers contain potassium hydroxide which traps carbon dioxide that is produced by respiration in solid form as potassium carbonate. When cells consume oxygen, the gas volume in the respirometer system decreases with no carbon dioxide to increase it back up, allowing scientists to calculate the amount of oxygen used using the ideal gas equation.</p>

<p>Cellular respiration is an important process that creates usable energy for organisms, therefore, studying the contexts in which it is improved or impeded is not only interesting, but also necessary. Especially, mitochondria are essential for cellular respiration and any conditions that affect mitochondrial health have immense consequences for the health of the organism. For instance, mitochondrial myopathies are a group of neuromuscular diseases which are caused by mitochondrial damage, affecting predominantly nerve and muscle cells, which require high levels of energy to function<sup>1</sup>. Moreover, many poisons work by inhibiting cellular respiration. For example, cyanide inhibits the production of ATP through oxidative phosphorylation, thus understanding the mechanisms cyanide or other metabolic poisons enables treatment of individuals who have been exposed to them<sup>2</sup>. Similarly, some medications such as certain antibiotics, chemotherapeutics, statins, and anesthetics can also interfere with mitochondrial function and may not be suitable to treat patients that have mitochondrial disorders<sup>3</sup>.</p>

<h4>References</h4>

<ol class="references">
	<li><strong>Lin, MT and Beal, MF.</strong> Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases. <em>Nature. </em>2006, Vol. 443, (787-95).</li>
	<li><strong>Beasley, DMG and Glass, WI.</strong> Cyanide poisoning: pathophysiology and treatment recommendations. <em>Occupational Medicine. </em>Vol. 48, 7 (427-31).</li>
	<li><strong>Finsterer, J and Segall, L.</strong> Drugs interfering with mitochondrial disorders. <em>Drug Chem Toxicol. </em>2010 , Vol. 33, 2 (138-51).</li>
</ol>


Cellular Respiration: Quantification using Microrespirometers - Concept

Autotrophs and Heterotrophs

Living organisms require a continuous input of energy to maintain cellular and organismal functions such as growth, repair, ...

JoVE Lab Manual

Biology

Cellular Processes

Cell Structure

<h4>Background</h4>
<p>Cells represent the most basic biological units of all organisms, whether it be simple, single-celled organisms like bacteria, or large, multicellular organisms like elephants and giant redwood trees. In the mid 19<sup>th</sup> century, the Cell Theory was proposed to define a cell, which states:</p>
<ul>
	<li>Every living organism is made up of one or more cells.</li>
	<li>The cells are the functional units of all organisms.</li>
	<li>All cells arise from preexisting cells.</li>
</ul>
<p>All cells share common features such as having a plasma membrane, a cytoplasm, DNA, and ribosomes. A plasma membrane is a phospholipid bilayer that surrounds the cell. This thin and fluid layer around the cells serves to isolate the cell&#8217;s contents from its environment and regulates the material exchange with its environment, while also facilitating interactions with other cells. Inside the plasma membrane, the cell is filled with a gel-like fluid called cytoplasm that contains organic molecules, salts, and other materials that are vital for the cell&#8217;s functions. Therefore, biochemical reactions that support life, which are known as metabolic processes, take place inside the cytoplasm. The types of metabolic processes that a cell can execute depend on its genetic information. All cells use DNA as the genetic material, which is the hereditary blueprint to construct cellular structures and products. Finally, all cells use ribosomes to synthesize their protein products.</p>
<p>There are two types of cells based on their genetic material location: prokaryotic, which means &#8220;before nucleus&#8221;, and eukaryotic, which means &#8220;true nucleus&#8221;. Therefore, while both types of organisms have DNA, prokaryotes like bacteria have nucleoids, or &#8220;nucleus-like&#8221; components instead of a nucleus, whereas eukaryotes possess true, membrane-bound nuclei to contain their DNA. Moreover, prokaryotes are relatively small, around 0.1&#8211;5.0 micrometers (&#181;m), in comparison to eukaryotes that can typically range from 10-100 &#181;m in size. The small size of prokaryotes allows quick and effortless distribution of materials within the cell and execution of metabolic processes, as well as swift removal of waste or other products from the cell. Hence, eukaryotic cells possess specialized structures known as organelles, such as mitochondria or Golgi apparatus, to enable the execution of vital functions.</p>
<h4>The Eukaryotic Cell</h4>
<p>The eukaryotic cell is a shared derived trait of all eukaryotes, meaning that it had a single origin that has since been inherited by all eukaryotes. The earliest eukaryotic cells are seen in fossils about 2.4 billion years ago, and are recognizable because they are larger than prokaryotic cells<sup>1</sup>. The origin of this cell type resulted from an endosymbiotic event in which one amoeba-like cell engulfed a micrococcal bacteria and formed a stable coexistence<sup>2</sup>. The engulfed bacteria evolved into the first energy-producing organelles, mitochondria, which are the aerobic metabolism organelles in the cell. Mitochondria have their own separate genome and are similar in size to prokaryotes. They contain two layers of membranes that enclose two distinct compartments. Some of the reactions that break down high-energy biomolecules occur in the inner compartment, whereas the outer compartment houses the reactions that capture the energy released from these compounds into adenosine triphosphate (ATP) molecules to be used as the energy currency of the cell.</p>
<p>Nuclei and mitochondria are not the only shared structures of eukaryotic cells. Other ubiquitous eukaryotic organelles are the smooth and rough endoplasmic reticulum (ER), Golgi apparatus, lysosomes and vacuoles. Endoplasmic reticulum simply means &#8220;network inside the plasma&#8221; and as its name indicates it is a large network of membranes inside the cell, especially around the nucleus. Parts of the rough ER extend from the nuclear membrane and are distinguished from the smooth ER by their rough appearance due to numerous ribosomes on their surface. Rough ER is the site for protein synthesis, such as the proteins that are embedded in the plasma membrane or the proteins that are secreted from the cell. In contrast, smooth ER produces lipid-based products but also contains enzymes to detoxify harmful chemicals. Hence liver cells contain abundant smooth ER. Also, muscle cells contain significant amounts of smooth ER because of the calcium-storing function of this organelle, which is essential for muscle contraction. The Golgi apparatus sorts, modifies, and packages cellular products inside vesicles, which fuse with the plasma membrane to release the products. Some of the proteins that are produced in the rough ER are intracellular digestive enzymes. These enzymes are packed in the Golgi apparatus into special vesicles called lysosomes. The major function of the lysosomes is to digest the food particles engulfed by the cell as well as old cell parts. Vacuoles are sacs of cell membrane that serve as storage units within cells. They may serve to store water to regulate the cell&#8217;s water content as well as store metabolic products or even poisonous molecules, depending on the cell type and the organism.</p>
<h4>Kingdom-specific Organelles</h4>
<p>Eukaryotic cells also developed distinct organelles, specific for each kingdom. For instance, kingdom Plantae and Animalia are both eukaryotic, however the organelles of plant and animal cells differ in key ways that allow them to carry out their lives as producers and consumers, respectively. Terrestrial plants need to grow tall and have rigid stems to hold leaves, which they use for photosynthesis. They also need to be able to retain water taken up by roots. Their cells reflect these specific needs. Unlike animal cells, plant cells have chloroplasts, which are used for photosynthesis and often contain the green pigment chlorophyll. Additionally, they are surrounded by cell walls, which are rigid outer layers made of cellulose to support growth and water retention. Because they need to store large amounts of water to maintain the water pressure in the cell, they have larger vacuoles than animal cells. In addition, plant cells also have another type of specialized storage organelles called plastids, which contain pigments as well as photosynthetic products such as starch. These differences are noticeable and distinguish plant cells from animal cells: plant cells generally have a regular, rectangular shape due to their rigid cell walls, while animal cells are rounded and more irregular.</p>
<h4>Microscopy</h4>
<p>Some cells, such as frog oocytes, are large enough to be seen with the naked eye, yet most cells cannot be seen without any visual aid. Therefore, scientists use microscopy techniques to study cell structures and distinguish cell types from one another. While microscopes are able to magnify objects that are difficult or impossible to be see with the human eye, most tissues naturally lack pigmentation. Therefore, solutions have been created that can selectively stain cells based on their molecular composition. This allows researchers to distinguish between organelles in a cell, tissue types in a plant stem, and fat layers in animals, just to name a few examples. Methylene blue dye stains nucleic acids of dead cells, binding to negatively charged DNA. Safranin solution is another biological dye that stains cell nuclei red. Cells only need to be in the staining solutions for a short period of time, and can be mounted immediately following the staining step. The commonly used mounting techniques are wet mount and oil immersion. A wet mount is created by collecting a sample and putting it on a glass slide with liquid between the slide and the coverslip. Cell samples are suspended in liquids like water or glycerol. Glycerol is better to use with live cultures, because it prevents the proliferation of bacteria<sup>3</sup>. Immersion oil can be added on top of the coverslip to improve viewing of the sample at high magnification. This is accomplished because the oil has the same refractive index as glass, which means that it allows light to pass through it as well as glass would. The glass-air interface scatters light more than oil or glass, so the clarity of the image is affected when samples are mounted &#8220;dry&#8221;, or without oil. Once the cells are stained and mounted, they are ready to be studied under the microscope.</p>
<p>There are various microscopy techniques from electron scanning technology that has allowed researchers to view objects on an atomic level to fluorescent live cell imaging that allows real-time monitoring of the movement of molecules within individual cells<sup>4</sup>. Bright-field microscopy is the simplest microscopy technique, requiring only a halogen source light, a condenser lens to focus the light, an ocular lens to view the image, and an objective lens to magnify the image. With any microscopy technique, it is important to understand the parts of a microscope before using one. In general, compound microscopes used for bright-field imaging have an eyepiece at the top of the scope, which is attached to the head and objectives. The eyepiece has a magnification of 10X, and objective lenses are set to a particular magnification in a range of 4X-100X. There are between three and five objectives on a standard microscope. The objectives point down to the stage, which is where a specimen is placed for viewing. The stage often has mechanical parts and stage clips to hold a slide and move it around while viewing. An aperture is a hole in the stage for light to pass through. This light is controlled by an adjustable condenser lens above an illuminator, or light source. To control the zoom of the stage for the object being viewed, microscopes feature coarse and fine focus adjustment knobs. The coarse focus knob moves on a larger scale than the fine focus, but they are on the same axis. The fine focus is useful when the object on the stage has been brought close to the objectives. It is important not to let the objective lens touch the object on the stage, as it can scratch the lens. Objects should always be first viewed on the lowest magnification objective and clearly focused before switching to higher magnification objectives.</p>
<p>Microscopy is an important tool for many aspects of the medical field including research, diagnosis, and treatment. This has the application of using nanotechnology in medicine, as a new treatment method in place of a more invasive surgery<sup>5</sup>. Surgeons also make use of microscopes, some of which have been modified to be mounted on a surgeon&#8217;s head and are operated with foot pedals. These are of much lower magnification than even the light microscopes used today, but they facilitate the safe execution of delicate procedures, such as optical and neurosurgery.</p>
<h4>References</h4>
<ol class="references">
	<li><strong>Bengtson S, Rasmussen B, Ivarsson M, Muhling J, Broman C, Marone F, Stampanoni M, Bekker A.</strong> Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt. <em>Nature Ecology &#38; Evolution. </em>2017, Vol. 1, Article number: 0141.</li>
	<li><strong>Vellai T, Vida G.</strong> The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. <em>Proc. R. Soc. Lond. B. </em>1999, Vol. 266, 1571-1577.</li>
	<li><strong>Gouet V, Roger G, Fonty C, Andre P.</strong> Effects of glycerol on the growth, adhesion, and cellulolytic activity of rumen cellulolytic bacteria and anaerobic fungi. <em>Current Microbiology. </em>24, 1992, Vol. 4, 197-201.</li>
	<li><strong>Cognet L, Leduc C, Lounis B.</strong> Advances in live-cell single-particle tracking and dynamic super-resolution imaging. <em>Curr Opin Chem Biol. </em>2014, Jun; 20:78-85.</li>
	<li><strong>Asiyanbola B, Soboyejo W.</strong> For the surgeon: an introduction to nanotechnology. <em>J Surg Educ. </em>2008, Vol. 65, 2 (155-61).</li>
</ol>

Cell Structure: Visualizing Onion and Human Cells - Concept

Background
Cells represent the most basic biological units of all organisms, whether it be simple, single-celled organisms like bacteria, or large, ...

Fundamentals

Extraction

Extraction: Liquid-Liquid and Acid-Base Extraction - Procedure

Source: Lara Al Hariri and Ahmed Basabrain at the University of Massachusetts Amherst, MA, USA

	Cellulose RecoveryExpand
	Extraction and filtration can ...

Chemistry

Lab Manual Sub Articles

Lab Techniques

<p>Source: Smaa Koraym at Johns Hopkins University, MD, USA</p>
<ol class="note-items">
	<li data-note-item="1" data-parent-collapse=""><strong>Determining the Density of an Egg</strong><button class="expand">Expand</button>
	<p>Density is a measure of how compact a substance or object is, and it is calculated as mass divided by volume. When a dense object is placed in a liquid with a lower density, the object sinks; when the object is less dense than the liquid, it floats. When the densities are the same, the object will be suspended in the liquid. In this experiment, we&#39;ll determine the density of an egg by creating a solution with the same density. We&#39;ll measure the density of the salt solution using different volume measurement glassware and determine which is the most accurate.</p>
	<ul class="lab-items">
		<li data-sub-note-item="1-1">
		<div class="lab-step">To begin, wear the appropriate personal protective equipment, including close-toed shoes, long pants, long-sleeved shirt, lab coat, chemical splash goggles, and gloves.</div>
		</li>
		<li data-sub-note-item="1-2">
		<div class="lab-step">Measure the mass of the egg. Set a weigh boat on the balance and tare it. Carefully set the egg in the weigh boat while you record the mass in your notebook.</div>
		</li>
		<li data-sub-note-item="1-3">
		<div class="lab-step">Prepare the salt solution that will be used to suspend your egg. Use the 600-mL beaker and fill it 3/4 of the way full with deionized water.</div>
		</li>
		<li data-sub-note-item="1-4">
		<div class="lab-step">Gently place your egg in the beaker, and then add about one teaspoon of NaCl into the water. Stir the solution gently until the NaCl dissolves. Continue to add NaCl until the egg floats just below the surface.</div>
		</li>
		<li data-sub-note-item="1-5">
		<div class="lab-step">Use different glassware to measure the volume of the salt solution. Weigh the 50-mL graduated cylinder on the top loading balance and record the mass. Then, measure 20 mL of your salt solution and record the volume in your notebook. <strong>Note: </strong>Place a blank sheet of paper behind the graduated cylinder to read the volume more clearly. Always view the measurement at eye level and measure the volume from the bottom of the meniscus. The lines on the graduated cylinder are 0.2 mL apart, meaning that you can read the volume to the hundredths place.
		<h4><b>Table 1: Measuring Mass</b></h4>
		<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
			<tbody>
				<tr>
					<td style="text-align: center;"><strong>Container</strong></td>
					<td style="text-align: center;"><strong>Mass of empty container (g)</strong></td>
					<td style="text-align: center;"><strong>Mass of full containter (g)</strong></td>
					<td style="text-align: center;"><strong>Mass of solution (g)</strong></td>
					<td style="text-align: center;"><strong>Percent error</strong></td>
				</tr>
				<tr>
					<td>50-mL graduated cylinder</td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
				</tr>
				<tr>
					<td>10-mL volumetric pipette</td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
				</tr>
				<tr>
					<td>50-mL beaker</td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
				</tr>
				<tr>
					<td>20-mL volumetric flask</td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
					<td style="text-align: center;"></td>
				</tr>
			</tbody>
		</table>
		<a href="https://www.jove.com/CDNSource/lm/labs/41/Table_1._Measuring_Mass.xlsx" target="_blank">Click Here to download Table 1</a></div>
		</li>
		<li data-sub-note-item="1-6">
		<div class="lab-step">Weigh the filled graduated cylinder and record the mass in your notebook. Then, pour the salt solution back into the 600-mL beaker.</div>
		</li>
		<li data-sub-note-item="1-7">
		<div class="lab-step">Use the volumetric pipette to measure volume. First, weigh the empty 50-mL beaker and record the mass in your notebook. Then, carefully measure 10 mL of the salt solution using the volumetric pipette and dispense the salt solution into the beaker.</div>
		</li>
		<li data-sub-note-item="1-8">
		<div class="lab-step">Measure another 10 mL and add it to the beaker. Weigh the filled beaker and record the mass in your notebook. Then, empty, rinse, and dry the beaker.</div>
		</li>
		<li data-sub-note-item="1-9">
		<div class="lab-step">Use the volumetric flask to measure volume. Weigh the empty 20-mL volumetric flask and record the mass. Then, carefully fill the flask with the salt solution to just below the 20-mL fill mark. Do not fill it all the way. Use an eyedropper to finish filling the flask so that the bottom of the meniscus just touches the fill line on the neck of the flask. Then, weigh the full flask and record the weight.</div>
		</li>
		<li data-sub-note-item="1-10">
		<div class="lab-step">Lastly, use the 50-mL beaker to measure volume. Weigh the empty beaker, then fill the beaker with salt solution to the 20-mL line and weigh the full beaker. Record the masses in your notebook.</div>
		</li>
		<li data-sub-note-item="1-11">
		<div class="lab-step">Measure the displacement of the egg when it is submerged in the salt solution. First, remove the egg and look at the level of the salt solution in the 600-mL beaker. <strong>Note:</strong> If it is not at a marked line, add deionized water to the solution so that the meniscus is at a readable volume and record the volume.&#160;
		<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
			<tbody>
				<tr>
					<td><strong>Measurements</strong></td>
					<td><strong>Salt solution using 20-mL volumetric flask&#160;</strong></td>
					<td><strong>Egg</strong></td>
				</tr>
				<tr>
					<td>Mass (g)</td>
					<td></td>
					<td></td>
				</tr>
				<tr>
					<td>Displacement of water (cm)</td>
					<td style="text-align: center;">-</td>
					<td></td>
				</tr>
				<tr>
					<td>Inner diameter of 600-mL beaker (cm)</td>
					<td style="text-align: center;">-</td>
					<td></td>
				</tr>
				<tr>
					<td>Volume (cm&#179;)</td>
					<td style="text-align: center;">-</td>
					<td></td>
				</tr>
				<tr>
					<td>Volume (mL)</td>
					<td style="text-align: center;">20</td>
					<td></td>
				</tr>
				<tr>
					<td>Density (g/mL)</td>
					<td></td>
					<td></td>
				</tr>
			</tbody>
		</table>
		<strong><a href="https://www.jove.com/CDNSource/lm/labs/41/Table_2._Measuring_Density.xlsx" target="_blank">Click Here to download Table 2</a> </strong></div>
		</li>
		<li data-sub-note-item="1-12">
		<div class="lab-step">Gently place the egg in the beaker.</div>
		</li>
		<li data-sub-note-item="1-13">
		<div class="lab-step">Use a ruler to measure the new height of the solution level and record the height. Then, place the ruler across the top of the beaker to measure the inner diameter.</div>
		</li>
		<li data-sub-note-item="1-14">
		<div class="lab-step">Calculate the new volume from these measurements. Subtract the initial volume to obtain the displacement of the egg (volume).</div>
		</li>
		<li data-sub-note-item="1-15">
		<div class="lab-step">To clean up from the experiment, return the egg to your instructor and pour the salt solution down the sink. Rinse all used glassware with tap water and set them out to dry. Finally, return the sodium chloride to your instructor.</div>
		</li>
	</ul>
	</li>
	<li data-note-item="2" data-parent-collapse=""><strong>Results</strong><button class="expand">Expand</button>
	<ul class="lab-items">
		<li data-sub-note-item="2-1">
		<div class="lab-step">Calculate the mass of the solution in each of the different volumetric glassware by subtracting the empty glassware mass from the full glassware mass.</div>
		</li>
		<li data-sub-note-item="2-2">
		<div class="lab-step">Keep track of uncertainty in your measurement by using significant figures. For example, when we look at the graduated cylinder measurement, the weight of the empty container is 90.92, and the weight of the full container is 111.59. The weight measurements have significant figures to the hundredths place, so it is important that significant figures are maintained throughout our calculations. Thus, the mass of the 20-mL salt solution is 20.67 g.</div>
		</li>
		<li data-sub-note-item="2-3">
		<div class="lab-step">The 50-mL beaker weighed 28.65 g when it was empty and 47.96 g when it contained 20 mL of salt solution. Therefore, the mass of 20 mL of the salt solution is 19.31 g.</div>
		</li>
		<li data-sub-note-item="2-4">
		<div class="lab-step">Repeat the calculation to obtain the mass of 20 mL of salt solution that was measured using the 10-mL pipette and the 200-mL volumetric flask.<b> Note:</b> Generally speaking, volumetric measurements are more accurate when using a volumetric flask.</div>
		</li>
		<li data-sub-note-item="2-5">
		<div class="lab-step">Look at the accuracy of the other methods compared to the volumetric flask in terms of percent error. Percent error is calculated by subtracting the theoretical value from the experimental value, then dividing by the theoretical value times 100.
		<ul>
			<li><img src="https://www.jove.com/CDNSource/lm/labs/41/41_Procedure_1b.jpg" /></li>
		</ul>
		</div>
		</li>
		<li data-sub-note-item="2-6">
		<div class="lab-step">Use the volumetric flask measurement as the theoretical value to determine the percent error for the other volume measurement methods. As expected, the volume measurement that uses the markings on the beaker is the least accurate.<strong> Note: </strong>We also know this because the known density of pure water is 1 g/mL. Thus, 20 mL of pure water weighs 20 g. The density of the salt solution must be higher than 20 g since salt was added to the water.</div>
		</li>
		<li data-sub-note-item="2-7">
		<div class="lab-step">Calculate the density of the salt solution using the volumetric flask measurement. Divide the mass of the solution by the volume of the solution. Thus, the density of the salt solution is 1.053 g/mL.</div>
		</li>
		<li data-sub-note-item="2-8">
		<div class="lab-step">Compare the calculated density of the salt solution to the density of the egg. The volume calculated using the displacement of water in a beaker was found to be 61.14 cm<sup>3</sup> or 61.14 mL. The weight of the egg was measured to be 60.15 g, so its density is 0.9838 g/mL. The disparity between the density of the egg and the density of the salt solution arises from error introduced in both calculations, primarily due to volume measurement readings.</div>
		</li>
	</ul>
	</li>
</ol>

Accuracy, Precision, Uncertainty, and Significant Figures - Procedure

Source: Smaa Koraym at Johns Hopkins University, MD, USA

	Determining the Density of an EggExpand
	Density is a measure of how compact a substance or ...

Extinction

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Diversity and Extinction during the Paleogene Epoch
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">Begin this procedure by reading the extinction reading supplement that has been printed out for you. <br /><strong>NOTE:</strong> Alternatively, you may download the reading supplement at the link below.&nbsp; <a href="https://www.jove.com/CDNSource/lm/labs/24/Lab_20_Reading Supplement.docx" style="display:block;margin:20px;" target="_blank">Click here to download the extinction reading supplement</a>
</div></li><li data-sub-note-item="1-2"><div class="lab-step">Using the information contained in the extinction reading supplements pertaining to the taxa of interest and the Chicxulub impact event, make predictions for each taxon listed in Table 1. Consider whether diversity in each taxon increased, decreased, or stayed the same immediately following the Cretaceous-Paleogene boundary and later on in the Paleogene epoch. <a href="https://www.jove.com/CDNSource/lm/labs/24/Table_1_Extinction.xlsx" style="display:block;margin:20px;" target="_blank">Click Here to download Table 1</a>
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Then, fill out the reasons for each of your predictions in the Contributing Factors column. HYPOTHESES: The experimental hypothesis is that many of the different taxa will show changes in diversity after the Cretaceous-Paleogene event, and again at the end of the Paleogene, with some increasing in diversity, while others decrease. The null hypothesis is that there will be no changes in diversity between taxa following the Cretaceous-Paleogene event, or at the end of the Paleogene.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Gather diversity data by going to the Paleobiology Database: <a href="http://www.paleobiodb.org" target="_blank">www.paleobiodb.org</a>.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">In the center of the screen, click the yellow box labeled Download Data. Under the italicized heading, &#8220;What do you want to download?&#8221;, select Diversity over time on the left side and Comma-separated values on the right side.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Scroll down to the heading &#8220;Select by taxonomy&#8221;.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">In the first box labeled 'Taxon or taxa to include', type in the name of the taxon that data is being gathered on.  NOTE: Ensure the spelling is correct.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">Now, go to the dropdown menu right below that box labeled &#8220;Taxonomic resolution&#8221;, and select genera.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Under the next heading, Select by time, type Maastrichtian into the first box and Chattian in the box directly below. Make sure the dropdown menu labeled Time rule is set to major and the Temporal resolution is set to stage.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Select &#8220;Assume extant taxa range through to present&#8221;. Scroll back up to the middle of the page and click download. A save window will open.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">Save the .csv file to a safe and accessible place and rename it to make it easy to identify.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Open the file and scroll down to the main dataset under Records.  NOTE: The data are arranged in reverse time order by geological stage. The second column, interval_name, gives the accepted name of the stage in question. The next two columns give the appropriate dates of the stage in millions of years before the present. The final column, number of occurrences, gives a total count of the genera extant during that geological stage as determined from occurrence of fossils.
</div></li><li data-sub-note-item="1-13"><div class="lab-step">To more easily work with this data, copy and paste each column into a new sheet. Be sure to label this sheet with the taxon in question, the data and time the data were obtained, and the data source.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">Repeat this process for each of the taxa in Table 1 (steps 4 &#8211; 12). NOTE: Data from multiple taxa can be kept on the same sheet, so long as they are kept distinct and labeled appropriately.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">To create line plots for each of the taxa showing the change in diversity over time, select the max_ma column and the number of occurrences column simultaneously.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">In Excel, select Insert from the top toolbar and find the section labeled Charts. Select the bottom center icon, Insert Scatter Chart.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Then, select the Scatter with Straight Lines and Markers and a graph should appear. NOTE: Since the axis of this graph is in units of millions of years ago, the axis is in the reverse direction of time when put in numerical order.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">To fix this, click on the green plus sign in the top-right corner of the graph and hover over Axes. This should reveal a small black arrow. Click the arrow to open up a small menu and select More Options.
</div></li><li data-sub-note-item="1-19"><div class="lab-step">This will open the Axis Options menu. Under Axis Options, click the box next to Values in reverse order. NOTE: It is also possible to change the axis scales from this menu, which can be used to eliminate the excess time that is not being analyzed in this lab. Keep any changes consistent between different graphs.
</div></li><li data-sub-note-item="1-20"><div class="lab-step">Double-click on the title at the top of the graph and change it to the taxon being represented.
</div></li><li data-sub-note-item="1-21"><div class="lab-step">Make a separate graph for each of the taxa in Table 1. Keep them organized and in one location. A separate sheet for graphs is recommended.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">For each graph, identify the location of the Cretaceous-Paleogene boundary and draw a vertical line through the graph at this point.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Using the information from the graphs, fill out Table 2. In some cases, it may be helpful to go back to the original dataset and compare actual values, particularly when they are small. <a href="https://www.jove.com/CDNSource/lm/labs/24/Table_2_Extinction.xlsx" style="display:block;margin:20px;" target="_blank">Click Here to download Table 2</a>
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Compare these values to the predictions made in Table 1 and discuss if the original contributing factors are still likely candidates.
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Using the dataset, calculate the percentage of total taxa that went extinct over the Cretaceous-Paleogene boundary using this equation.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">There is an event in the middle of the Paleogene known as the Paleocene-Eocene Thermal Maximum about 55.5 million years ago. This represents a high point in temperature during the Paleogene epoch at approximately 8 &#176;C higher than today&#39;s average temperature. Does this point seem to have an effect on diversity for any of the taxa? If yes, then which ones?
</div></li></ul></li></ol>

Extinction: Diversity and Extinction during the Paleogene Epoch - Procedure

Diversity and Extinction during the Paleogene Epoch
ExpandBegin this procedure by reading the extinction reading supplement that has been printed out for ...

Ecology

Microbial and Fungal Diversity

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Examining Microbial Colony Structures
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">To begin, collect your allocated culture plates and then remove the Parafilm and lid from one of them.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">Place the uncovered plate under a dissecting microscope and then observe the individual communities within each quadrant of the plate.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">As the colonies are identified, fill out the observed colony properties in the appropriate column in the table.  <a href="https://www.jove.com/CDNSource/lm/labs/28/Table_1_Microbial_diversity.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 1</a>
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Then, repeat the observations for each of the other two bacterial species.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">To perform Gram staining of your three bacterial species, first label the ends of three microscope slides with the initials of each bacteria species, your initials, and the date. HYPOTHESES: In this experiment, the experimental hypothesis might be that it is possible to elucidate different bacterial species and shapes using Gram staining, and that Gram-positive bacteria will stain purple with crystal violet whereas Gram-negative bacteria will appear pink due to the safranin counterstain. The null hypothesis could be that all of the bacterial types will retain both stains equally, and staining will not help elucidate their species or shape.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">To begin the first stain, attach a clip to the slide for ease of handling. For each bacterial smear, remember to be sure to use a cleaned and flame-sterilized inoculating loop.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Place two loopfuls of sterile distilled water onto the center of the slide.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">After sterilizing the loop again, cool the loop by touching an uninoculated portion of the agar several times.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Then, remove a small amount of culture from an isolated colony and mix it with the water on the slide.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Allow the slide to dry at room temperature and heat-fix the smear by quickly passing it through a flame.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">Once dry, pipette several drops of crystal violet onto the slide and let it sit for two to three minutes.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Carefully rinse the slide with distilled water by aiming the direct flow towards the top of the slide, allowing the water to gently flow down. Do not aim the water flow directly at the smear.
</div></li><li data-sub-note-item="1-13"><div class="lab-step">Next, cover the slide with Gram&#39;s iodine, leave it to sit again for two minutes, and then gently rinse with distilled water.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">Decolorize the slide with 95% ethanol until stain no longer washes away.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">Immediately, rinse the slide with distilled water. This will limit over-decolorizing.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Then, add several drops of safranin counterstain and leave for 30 s. This will stain any Gram-negative cells present.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Gently rinse the slide with distilled water and blot dry with absorbent paper.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">After staining the other two slides in the same manner (steps 6 &#8211; 17), observe each with a microscope.
</div></li><li data-sub-note-item="1-19"><div class="lab-step">Use a low power objective first to make coarse adjustments. When you find an ideal section, move on to the higher magnifications.
</div></li><li data-sub-note-item="1-20"><div class="lab-step">After further imaging and adjusting the smear with a medium power objective, add immersion oil directly to the smear. NOTE: The oil is needed for high power objectives that will provide the best micrographs.
</div></li><li data-sub-note-item="1-21"><div class="lab-step">Now, use colored pencils to draw the observed bacteria in the appropriate magnification circles and fill in the observed characteristics in the appropriate column, noting the bacteria&#39;s shape and whether it is Gram-positive, identified by darker purple staining, or Gram-negative, identified with pink staining. <a href="https://www.jove.com/CDNSource/lm/labs/28/Table_2_Microbial_diversity.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 2</a>
</div></li><li data-sub-note-item="1-22"><div class="lab-step">Finally, repeat the observation, drawing, and characterization for the other two stained bacterial slides.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Examining Fungal Structures
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">Remove the <em>S. cerevisiae</em> plate from the incubator and place a drop of water onto a microscope slide.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Using a sterilized inoculating loop, smear a film of yeast into the drop of water and place a cover slip over the slide.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Place the slide under the microscope at the lowest magnification, increasing the magnification to the oil immersion setting to see the individual yeast cells.
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Observe the general shape and structure of the yeast and identify any cells that are undergoing asexual reproduction by budding.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Now, draw the cells in the appropriate magnification circles.
</div></li><li data-sub-note-item="2-6"><div class="lab-step">When you are done observing the yeast, replace the <em>S. cerevisiae</em> slide with a prepared Ascomycetes apothecium slide and set the microscope to the lowest magnification.
</div></li><li data-sub-note-item="2-7"><div class="lab-step">Using colored pencils, draw the structures at low and high magnifications, including the asci and ascospores.
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Finally, place a button mushroom, <em>Agaricus bisporus</em>, under the dissecting microscope and draw the features, including the pileus, or cap, the gills, and the stipe, or stalk.
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Using the coloring of the bacteria recorded in the table, determine which species are Gram-positive and which are Gram-negative.
</div></li><li data-sub-note-item="3-2"><div class="lab-step">Then, look at the shapes recorded in the table to determine which bacterial species are bacillus, coccus, or spirillum.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Next compare your illustrations of the yeast cells to your illustrations of the bacterial cells. NOTE: Yeast from the Ascomycetes phylum, such as <em>S. cerevisiae</em>, can reproduce asexually, which can be observed through the budding of the cells under a microscope.
</div></li><li data-sub-note-item="3-4"><div class="lab-step">Record any observations of yeast cells budding.  NOTE: Ascomycetes can also reproduce sexually via mitosis and haploid spore formation.
</div></li><li data-sub-note-item="3-5"><div class="lab-step">Record any observations of spore or asci formation you observed in the table.
</div></li><li data-sub-note-item="3-6"><div class="lab-step">NOTE: Fungus from the Basidiomycota phylum exhibit clearly observable gills under the pileus.
</div></li><li data-sub-note-item="3-7"><div class="lab-step">Record any fungal species that demonstrated gills under the pileus.
</div></li></ul></li></ol>

Microbial Colony and Fungal Diversity - Procedure

Examining Microbial Colony Structures
ExpandTo begin, collect your allocated culture plates and then remove the Parafilm and lid from one of them.
Place ...

Evolution

Animal Behavior

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Making Choice Chambers
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">Before beginning the experiments, use one of the Sharpies from the lab table to trace a line around the circumference of the bottom of both bottles. One line should be 1 cm from the base of the bottle and the other should be 1.5 cm from the base of the bottle.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">Use a razor blade to make a small cut in each bottle at the mark. 
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Then, insert the scissors and carefully cut along the line until the bottoms of the bottles are removed completely.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Fit one bottle bottom into the other.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Tape the bottles together to make a secure chamber.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Use the razor blade and scissors to poke a hole into the center of the chamber. 
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Take a piece of tape and fold the edge onto itself to make a tab and place the tape over the hole.  Note: The tab helps with easy removal and reattachment of the tape to the chamber.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">Use the Sharpie to label one side of the chamber A and the other side B.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Upon receiving the colony of <em>Drosophila</em>, perform a count to make sure there are 40 living individuals in the vial.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Geotaxis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">To perform a geotaxis assay, first attach a clean, empty bottle cap to each end of the choice chamber and turn the fly vial upside down onto its lid.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Open the tape flap in the center of the choice chamber.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Insert the funnel into the hole and tap all of the flies into the chamber. HYPOTHESES: The alternate hypothesis is that more flies will be moving against gravity, or up, regardless of the orientation of the choice chamber. Alternatively, if the flies are positively geotactic, then more flies will move down, or with gravity. The null hypothesis is that the flies will have no preference with regard to gravity and will move randomly within the chamber. 
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Once the <em>Drosophila</em> are in the chamber, close the tape flap, rotate the chamber so that it stands vertically with side A on the bottom, and start the timer.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Immediately, count the number of <em>Drosophila</em> that are moving up and the number that are moving down. Record these data for time point 0 in the table. 
</div></li><li data-sub-note-item="2-6"><div class="lab-step">After 30 seconds, rotate the chamber so that side B is on the bottom and count the number of <em>Drosophila</em> that are moving up or down. Record these data for time point 30 in the table.
</div></li><li data-sub-note-item="2-7"><div class="lab-step">After 60 seconds, rotate the chamber so that side A is on the bottom again and record the number of moving flies for time point 60.  <a href="https://www.jove.com/CDNSource/lm/labs/15/Table_1_Animal_behavior.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 1</a>
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Hold the chamber over the fly vial and carefully open the cap to return all of the <em>Drosophila</em> back to their empty vial. 
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Phototaxis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">To perform a phototaxis analysis, first cover side A of the choice chamber with tin foil, taking care that the foil reaches to the exact center between the two sides. 
</div></li><li data-sub-note-item="3-2"><div class="lab-step">Ensure the caps are secured on both ends of the chamber.  HYPOTHESES: In this exercise, the alternative hypothesis is that more flies will be found in the light side of the choice chamber, if the flues are attracted to light, or on the dark side if they are repelled by light. The null hypothesis is that <em>Drosophila</em> will have no preference with regard to either stimulus. Therefore, equal numbers of flies will be found on either side of the choice chamber.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Open the tape flap in the center of the choice chamber, insert the funnel into the hole, and tap all 40 flies into the chamber as previously described.
</div></li><li data-sub-note-item="3-4"><div class="lab-step">Set the timer to sound an alarm at 10 minutes.
</div></li><li data-sub-note-item="3-5"><div class="lab-step">When the alarm sounds, stop the timer, and count the number of flies in the open side B of the chamber.
</div></li><li data-sub-note-item="3-6"><div class="lab-step">Subtract that number from the total number of flies added to the choice chamber to calculate the number of flies in the covered side A.
</div></li><li data-sub-note-item="3-7"><div class="lab-step">Record these data in the table for time point 10.  <a href="https://www.jove.com/CDNSource/lm/labs/15/Table_2_Animal_behavior.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 2</a>
</div></li><li data-sub-note-item="3-8"><div class="lab-step">Carefully, return all of the flies back to their empty vial.
</div></li></ul></li><li data-note-item="4" data-parent-collapse="">Chemotaxis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="4-1"><div class="lab-step">HYPOTHESES: In this exercise, the alternative hypothesis is that more flies will be found on the side of the chamber with the apple cider vinegar if the flies are attracted to the odor. Or, if the flies are repelled by the vinegar, then more of them will be found on the side of the chamber presenting the odorless water. The null hypothesis is that <em>Drosophila</em> will have no preference with regard to either stimulus and will move randomly in the chamber.  Use an individual disposable plastic pipette to dispense two drops of the apple cider vinegar onto one cotton ball for side A of the chamber. 
</div></li><li data-sub-note-item="4-2"><div class="lab-step">Use an individual disposable plastic pipette to dispense two drops of the distilled water onto a cotton ball for side B of the chamber. 
</div></li><li data-sub-note-item="4-3"><div class="lab-step">Fold two pieces of tape over themselves to create individual pieces of double-sided tape and use the tape to attach each cotton ball to the inside of the single bottle cap.
</div></li><li data-sub-note-item="4-4"><div class="lab-step">Screw the bottle caps with the cotton balls onto their corresponding sides of the chamber.
</div></li><li data-sub-note-item="4-5"><div class="lab-step">Transfer all of the flies into the chamber and set the timer to sound an alarm after 10 minutes. 
</div></li><li data-sub-note-item="4-6"><div class="lab-step">When the alarm sounds, stop the timer and record the number of flies in each side of the chamber. <a href="https://www.jove.com/CDNSource/lm/labs/15/Table_3_Animal_behavior.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 3</a>
</div></li><li data-sub-note-item="4-7"><div class="lab-step">At the end of the final experiment, funnel the flies into a morgue tube containing 70% ethanol. 
</div></li><li data-sub-note-item="4-8"><div class="lab-step">Dismantle the choice chambers for recycling.  NOTE: Since all of the chemicals used in these experiments are lab safe, the liquids can be disposed of down the sink, the chambers rinsed, and the solids can be thrown away in the trash. 
</div></li></ul></li><li data-note-item="5" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="5-1"><div class="lab-step">Gather all of the data collected for the geotaxis, phototaxis, and chemotaxis experiments.
</div></li><li data-sub-note-item="5-2"><div class="lab-step">Plot these values as bar graphs for different conditions and different time points.
</div></li><li data-sub-note-item="5-3"><div class="lab-step">Use these data to draw inferences about the behavior of <em>drosophila melanogaster</em>. 
</div></li></ul></li></ol>

Animal Behavior: Studying Taxis Behavior of Drosophila - Procedure

Making Choice Chambers
ExpandBefore beginning the experiments, use one of the Sharpies from the lab table to trace a line around the circumference of the ...

Cell Division

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Observing the Cell Cycle in a Root Tip
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">Hypotheses: The experimental hypothesis is that in root tips slices that have been treated with nocodazole, a chemical that interferes with microtubular polymerization, all of the cells will be arrested at the same stage of the cell cycle and that in untreated onion tip slices all of the different stages of the cell cycle will be visualized. The null hypothesis is that there will be no differences in mitosis between the two groups and that different stages of the cell cycle will be visualized. 
</div></li><li data-sub-note-item="1-2"><div class="lab-step">To prepare for this experiment you will use an onion that has been placed in water for several days until new white root tips have begun to sprout. Use a razor blade to cut a 1 cm piece from the end of one of the root tips. 
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Place the slice of onion into a microcentrifuge tube labeled &#8220;N&#8221; for the nocodazole condition. 
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Then, cut a second 1 cm piece of onion root tip and place in a microcentrifuge tube labeled &#8220;C&#8221; for the control condition.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Add 2 &#181;L of the 5 mg/mL nocodazole to 1 mL of water in the microcentrifuge tube labeled N and 1 mL of water only to the tube labeled C. 
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Leave the tubes containing the root tips to incubate for 12 hours and wipe down the workspace with 70% ethanol.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">When incubation is complete, set a heat block to 60 &#186;C.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">Wash the nocodazole treated tips with water and then aspirate the liquid.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">Repeat this wash two more times, for a total of three washes. 
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Fill both tubes with 1 mL of one normal hydrochloric acid. Incubate the tubes in a 60 &#186;C heat block for 12 - 15 min, then discard the acid into a waste flask.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">Now, add 1 mL of distilled water drop wise to the tubes at least three times to rinse the samples.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Now add one microliter of DAPI stain to 10 mL of phosphate buffered saline (PBS).
</div></li><li data-sub-note-item="1-13"><div class="lab-step">Then place 50 &#181;L of this dilute DAPI stain into each tube, and leave them at room temperature to incubate for 12 min. 
</div></li><li data-sub-note-item="1-14"><div class="lab-step">After this, preform three distilled water washes as in step 10. 
</div></li><li data-sub-note-item="1-15"><div class="lab-step">Label one microscope slide as 'Control' and another as 'Nocodazole'. 
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Transfer the stained roots onto their respective microscope slides and add a drop of water to the control slide and a drop of nocodazole to the nocodazole slide.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Use the razor blade to remove the unstained portions of each root tip and place a glass cover slip over each sample.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">Carefully press down on each cover slip with a gloved fingertip, and then let the slides sit for 10 min. 
</div></li><li data-sub-note-item="1-19"><div class="lab-step">Finally, view the slides under the 40X objective of a fluorescence microscope and capture images of your root tip cell preparations.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Understanding the Loss of Cell Cycle Control
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">NOTE: Before cells can pass through all of the stages of the cell cycle there are several checkpoints they must go through. These checkpoints are regulated by cyclin and cyclin-dependent kinase proteins, or CDKs. If the cyclins and CDKs determine that previous cellular events have not been adequately completed they will arrest the cells at this step and prevent them from proliferating. In cancer cells one or several of these molecular restraints for regulating cell division are lost and this allows the damaged cells to escape from cell proliferation control. These abnormal cells develop into tumors which are masses of uncontrolled proliferating cells that interfere with the normal functions of the body. Notice how before it divides this cancer cell rounds up and refracts light very strongly under the light microscope. This is because not all cancer cells successfully divide into daughter cells after each round of mitosis. This will mean that they often contain an excess of organelles and DNA and this increase in cellular content means they will refract light more intensely than normal cells do. 
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Examine your collected images and record in Table 1 the different cell structures and stages that could be identified in the onion tip slice that was treated with nocodazole. <a href="https://www.jove.com/CDNSource/lm/labs/10/Table_1_Cell_division.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 1</a>
</div></li><li data-sub-note-item="3-2"><div class="lab-step">If there are any cells undergoing mitosis, note what stages of cell division you see.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Record the percentage of cells in each stage of mitosis in Table 1. 
</div></li><li data-sub-note-item="3-4"><div class="lab-step">Next, examine the images of the untreated onion tip slice, and record what cell structures can you identify. 
</div></li><li data-sub-note-item="3-5"><div class="lab-step">If there are any cells undergoing mitosis, consider what stages of cell division you see, and record the percentages of cells in each stage of mitosis in the Table 1. 
</div></li></ul></li></ol>

Cell Division: Observing Cell Cycle in a Root Tip - Procedure

Observing the Cell Cycle in a Root Tip
ExpandHypotheses: The experimental hypothesis is that in root tips slices that have been treated with nocodazole, a ...

Genetics of Organisms

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">REF and WEF Fly Genetics
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">To prepare for the experiment, be sure to obtain cultures of <em>Drosophila melanogaster</em> at least two weeks ahead of the planned experiment day. NOTE: Because adult females store sperm after mating, you will need this time to generate virgin females by breeding the flies.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">You should get two stock cultures: wildtype, that is homozygous dominant red eyed flies, and white chromosome one mutant, which are homozygous recessive white eyed flies.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Purchase or create <em>Drosophila </em>habitats consisting of a clean vial, 3 cm of prepared food media, and a stopper to close the open end of the vial.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">When not being moved or counted, keep the flies in an incubator or room kept at 23 - 25 &#176;C, where the lifecycle will take around 12 days. NOTE: From the egg, <em>Drosophila </em>progress through four main stages of development: embryo, larva, pupa, and adult. The complete lifecycle takes about 10 days at 25 &#176;C, but it can be affected by temperature. For example, at 18 &#176;C, the lifecycle is about 19 days and at 29 &#176;C, the lifecycle is only seven days.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">As an overview, to set up for the student experiment, you will generate vials for each student group containing white eyed virgin female flies only, white eyed males only, red eyed virgin females only, and red eyed males only. These will be referred to as the experimental vials.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">When your vials from the supplier arrive, referred to as the stock vials, these will contain a mix of male and female flies, as well as larvae, pupae, and eggs.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Beginning with your stock vials, you will take around 3 - 5 males and the same number of females, keeping white eyed and red eyed flies separate at all times, and place these together into a new nursery vial containing food. NOTE: You can sex the flies using a magnifying glass. Look at the posterior of the fly. Males are slightly smaller and have darker solid pigment on the end of their abdomen. Females are larger and have stripes rather than a solid spot.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">You will leave the flies in these nursery vials for around 3 - 5 days to mate and lay eggs.
</div></li><li data-sub-note-item="1-9"><div class="lab-step">After this, you will move them back to their stock vials.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">Next, you will observe as the eggs and larvae in the nursery vials mature, checking the vials every 6 - 8 hours. As it takes females around 8 - 10 hours to become sexually mature, this should ensure that any females found in the nursery vials are virgin.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">As the new adult flies appear, you should transfer them from the nursery to the appropriate experimental tube. For example, if it is a male, transfer it to the experimental male tube for the appropriate eye color. If it is a female, it should be placed in an experimental vial labeled with eye color and virgin female.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">Keep adding flies to the appropriate vials until each experimental vial has at least five flies. NOTE: You will need to make enough experimental vials so that each student group has one of each eye color type and sex, with a few class spares. You should create enough nursery vials to account for this. A good rule of thumb is that it generally takes about two weeks for 25 healthy adults to produce about 50 new adults.
</div></li><li data-sub-note-item="1-13"><div class="lab-step">To begin the process, first label empty habitats to make the nursery vials to raise larvae and pupae for each strain of flies: red eyed and white eyed.
</div></li><li data-sub-note-item="1-14"><div class="lab-step">To move the adult flies into the nursery vial to lay eggs, use an anesthesia wand according to the manufacturer&#39;s instructions, placing it into the stock vial of mature flies. Wait until the animals become unconscious. Now they can be gently tapped onto a piece of white paper and sorted into piles of the same sex using a brush.
</div></li><li data-sub-note-item="1-15"><div class="lab-step">Transfer a few male and female flies to the appropriate vial labeled with their eye color phenotype and sex.
</div></li><li data-sub-note-item="1-16"><div class="lab-step">Place the nursery vials to incubate at 23 to 25 &#176;C and the flies will lay eggs.
</div></li><li data-sub-note-item="1-17"><div class="lab-step">Remove the adults after 3 - 4 days using anesthesia and put them back into the stock vial.
</div></li><li data-sub-note-item="1-18"><div class="lab-step">Remove any adult flies that have eclosed in the 6 - 8 hour period using an anesthesia wand.
</div></li><li data-sub-note-item="1-19"><div class="lab-step">Then, tip out the adults onto paper and sort them into groups based on their sex before placing each fly into an appropriate experimental vial marked male or virgin female and red or white for the phenotype. NOTE: Each experimental vial should contain five flies. Once this number is reached, then a new vial should be started. If you miss the 6 - 8 hour window, females may not be virgins, so these should be discarded into a morgue tube containing 70% ethanol or returned to the stock vial. Males do not need to be virgins, but do need to be kept in male only containers.
</div></li><li data-sub-note-item="1-20"><div class="lab-step">Each lab group will need one tube of five virgin red eyed females, one of five virgin white eyed females, one tube of red eyed males, and one of five white eyed males. In addition, they will need a morgue vial containing ethanol, two anesthesia wands, fly anesthetic, a paintbrush, a magnifying glass, some plain paper, and two empty fly vials for crosses.
</div></li></ul></li></ol>

Genetics of Organisms: REF and WEF Fly Genetics - Prep

REF and WEF Fly Genetics
ExpandTo prepare for the experiment, be sure to obtain cultures of Drosophila melanogaster at least two weeks ahead of the ...

Genetics

Plant Diversity

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Viewing Prepared Slides
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">To start the exercise, first split up into groups and find a station with a compound microscope, dissecting microscope and one prepared slide.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">HYPOTHESES: The alternative hypothesis for this experiment might be that plants have specific adaptations that allow them to survive and reproduce in their own individual terrestrial environments. The null hypothesis for this experiment is that all plants have the same adaptations to live in terrestrial habitats.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Find the prepared slide at your station and place it on the stage of the compound microscope. Then, secure it between the stage clips.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Next, find the light switch on the side or back of the microscope and turn it on to illuminate the slide from below.
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Adjust the lenses until the 10X lens is positioned above the slide.
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Now, look through the eye piece of the microscope and turn the large course adjustment knob on the side of the microscope to bring the slide into focus.
</div></li><li data-sub-note-item="1-7"><div class="lab-step">After course adjustment, the smaller fine adjustment knob can be used to further refine the focus. Do this until the material on the slide becomes clear.
</div></li><li data-sub-note-item="1-8"><div class="lab-step">For each slide there are several key structures that you will need to sketch in Table 1. <a href="https://www.jove.com/CDNSource/lm/labs/26/Table_1_Plant_diversity_and_evolution.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 1</a>
</div></li><li data-sub-note-item="1-9"><div class="lab-step">For moss antheridium, identify the areas where sperm are formed. These areas should be darker than surrounding regions and oblong in shape. Sperm are released from these structures and swim to the archegonia.
</div></li><li data-sub-note-item="1-10"><div class="lab-step">For moss archegonia, identify the eggs. These are circular in shape and are located at the bottom of a long dark tube called the vent. Once fertilized, the new embryo will be retained within the structures surrounding the egg for protection.
</div></li><li data-sub-note-item="1-11"><div class="lab-step">Then, for the onion stomata, identify the stomata. These are the circular structures with two dark spots on either side. These dark spots are the nuclei of the guard cells that surround the pore and control its opening and closing.
</div></li><li data-sub-note-item="1-12"><div class="lab-step">For conifer pollen grains, notice the two wings on either side of each pollen grain. These allow the pollen to be blown by the wind to the female ovule. Also, notice the dark spots within the pollen grain. These are the nuclei.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Observing Adaptations and Collecting Samples
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">NOTE: For this experiment, you&#39;ll be testing the same hypotheses, but you will leave the lab behind and venture outside to explore plant adaptations in the local environment. For safety, make sure to wear proper clothing and sun protection if needed.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Once your instructor has taken you to the designated outdoor location, try to identify plants in each of the three major groups: non-vascular, seedless vascular, and seeded vascular.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Using Table 2, fill out information for at least 10 plants listing the major group, specific adaptations and a brief sketch for each. <a href="https://www.jove.com/CDNSource/lm/labs/26/Table_2_Plant_diversity_and_evolution.xlsx" style="display:block;margin:20px;" target="__blank">Click Here to download Table 2</a>
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Where possible, try to identify different adaptations than the ones we&#39;ve discussed so far. These include traits such as leaf size and shape, plant height, or flowers. To find plants of all three major groups, you may need to look in more than one location or habitat.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Before returning to the lab, each group member should collect a leaf, flower or other structure from a plant of their choosing for further analysis.
</div></li><li data-sub-note-item="2-6"><div class="lab-step">Back in the lab, place the one group member&#8217;s specimen on the stage of the dissecting microscope.
</div></li><li data-sub-note-item="2-7"><div class="lab-step">Next, find the light switch and turn it on to illuminate the sample.
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Similar to the compound microscope, you will next need to adjust the fine focus knobs to bring the sample into view.
</div></li><li data-sub-note-item="2-9"><div class="lab-step">For leaves, view the stomata under maximum magnification. These will look like very small dots on the surface of the leaf.
</div></li><li data-sub-note-item="2-10"><div class="lab-step">Next, tear the leaf in half and see if you can find the clear cuticle that covers the surface of the leaf.
</div></li><li data-sub-note-item="2-11"><div class="lab-step">Examine the venation of the leaf, which allows for transport of resources.
</div></li><li data-sub-note-item="2-12"><div class="lab-step">When observing flowers, look for pollen, which will appear as yellow dust on the anthers of the flower.
</div></li><li data-sub-note-item="2-13"><div class="lab-step">Next, identify the stigma, a long structure protruding from the flower and ending with a round sticky tip. This is where pollen would land allowing sperm to travel down to the ovule at the base of the flower to form a seed.
</div></li><li data-sub-note-item="2-14"><div class="lab-step">Notice whether or not there is evidence of a fruit or seed in the base of the flower.
</div></li><li data-sub-note-item="2-15"><div class="lab-step">Make a sketch of each of the samples within your group.
</div></li><li data-sub-note-item="2-16"><div class="lab-step">When the exercise is complete, turn off the light on both microscopes. Remove the prepared slide from the stage of the compound microscope and return it to the instructor.
</div></li><li data-sub-note-item="2-17"><div class="lab-step">Finally, remove the samples you collected from the dissected microscope and discard them into the trash and clean the microscope stages, if necessary.
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Results
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Compare the adaptations you observed for the plants you examined outdoors with the adaptations other student groups noticed.
</div></li><li data-sub-note-item="3-2"><div class="lab-step">Take note of any similar adaptations across the different plant species.
</div></li></ul></li></ol>

Plant Diversity: Plant Adaptations across Different Species - Procedure

Viewing Prepared Slides
ExpandTo start the exercise, first split up into groups and find a station with a compound microscope, dissecting microscope and ...