Tuesday, May 20, 2014

Dissection Post


External Organs:

First Dorsal Fin- helps fish swim, provides stability 
Second Dorsal Fin- helps fish swim, provides stability 

Internal Organs: 

Gills- allow water to flow freely with oxygen and ammonium as it goes in and out of the fish
Muscle Segment- helps fish move efficiently 
Anus- fecal matter is ejected from the body 
Stomach- receives food to be digested 
Swim Bladder- allows fish to remain buoyant at specific depths 
Intestine- absorption of nutrients is carried out and waste is transformed into fecal matter 
Spleen- impurities in blood destroyed here 
Urinary Bladder- urine from kidney gathers here before being evacuated through urogenital aperture 
Urogenital aperture- opening to genital/urinary tracts allowing evacuation of gametes and urine 
Pyloric Caecum- digestive tract where part of digestion mainly occurs. Fermentation sometimes occurs here too. 
Kidney- eliminates metabolic waste and maintains pressure of initial fluids 
Liver- secretes bile and other substances 

Link to dissection video: http://youtu.be/uCVIQx5MN1Y


External Anatomy:
The crayfish is made up of 2 parts
The cephalothorax is made up of the head and thoracic 
The abdomen is the lower part of the crayfish.
Antenna: they use this to gather sensory information. (touch, taste, and smell)
Antennule: they use for balance and gathering sensory information (touch and taste) 
Cheliped: These are their large front claws. They help capture prey and can be used for defense. 
Walking legs:  Used for moving.
Swimmerets: They help create water currents and assist in reproduction 

External Anatomy cont.
Telson: its job is to hold the anus. 
Uropod: it is a segment of the cray fish and it contains the telson.
Telson + Uropod = makes the tail fan. This helps propel the crayfish backwards because cray swims  backwards. 
How to tell if it is boy or girl
This can be identified in the walking limbs. Using magnifying glass look at  the base of the leg. 
If you see a crescent shape slit it is a girl 
On the 4th walking leg there is a slit for the sperm duct opening, that means it is a boy

Internal Anatomy
Flexor muscle: It helps move the abdomen. It lines a majority of the abdomen. It is a powerful force when the cray fish needs to move backwards 
Gills: The gills are used to let carbon dioxide and oxygen to exchange, gills help them breath.
Green Gland: they accept waste from cellular waste, they then excrete the waste though the antennas pores. 
Brain: used for maintaining  homeostasis and other processing functions. 
Digestive gland: They make digestive juices and in these gland nutrients absorption takes places. 
Intestine: undigested nutrients goes to here. 
Tail muscles: this muscle is to help propel the crayfish

Link for dissection video: http://www.youtube.com/watch?v=siRSnEbFeyQ



Anterior and posterior ends of the clam- muscles that pulls the valves together 
Umbo- bump at the end of the anterior end which shields the clam. This is the oldest part of a clam (where it first started to grow)
Growth rings- tell how old a clam is by how many rings it has
Hinge ligament- keeps the clam together when it opens up
Ventral- the shell that protects the clam's soft body inside by surrounding around the outside


Gills- essential for almost all sea life in order to breathe. It is one of the clam's respiratory organs
Posterior & Anterior Adductor- by relaxing and contracting these muscles, it allows for movement of the clam 
Exhalant siphon- expels water and waste out of the clam
Inhalant siphon- brings in oxygen, food, and water into the clam

Mantle- forms outer wall of clam, and it encloses it's internal organs
Tooth- allows for the breakdown of a clam's food 

Incision Guide
Not many places you need to cut, all you really have to do it open it!!
A scalpel is ideal for cutting, you will need to cut through the clam's muscles along the side a little bit. Clams can be very stubborn, don't strain yourself because of its strong seal! Ask a teacher for assistance if you are unable to open it.

Link for video on how to dissect: http://youtu.be/50U8o_661-g




spinal cord: (not pictured) component of the nervous system made up of a soft fatty substance


heart: muscular organ helping blood to circulate.


gallbladder: small reservoir in which bile secreted by the liver collects before being discharged into the intestine during digestion.


liver: gland secreting bile that contributes to digestion.


pancreas: digestive gland connected to the intestine that produces secretions and hormones.


stomach: dilated section of the digestive tract before the intestine; it receives food to be digested.


small intestine: long thin portion of the digestive tract behind the stomach in which most of the digestion and food absorption take place.


large intestine: short wide portion of the digestive tract beforethe cloaca in which a small part of digestion and elimination of waste take place.


urinary bladder: (not pictured) reservoir where urine from the kidneys collects before being evacuated by the cloaca.


cloaca: (not pictured) orifice common to the intestine and the genital and urinary tracts; it is located at the end of the digestive tract.


spleen: (not pictured) organ of the circulatory system where impurities in the blood are destroyed.


kidney: (not pictured) organ secreting urine; it eliminates toxic substances from the body.


testis: (not pictured) male genital gland producing sperm.


lung: respiratory organ made of an extensible tissue; it forms a sac into which air inhaled through the nostrils is carried. A frog also breathes through its skin.


brain: (not pictured) main organ of the nervous system consisting of nerve centers; it is located in the upper portion of the head.


esophagus: (not pictured) canal of the anterior portion of the digestive tract; it carries food to the stomach.


tongue: (not pictured) movable mouthpart having gustatory and prehensile functions.



hind limb: long powerful articulated member attached to the terminal end of the trunk; it has five webbed toes used for walking, jumping and swimming.

webbed foot: each of the digits of the foot, connected by membranes; when spread, they make swimming easier.

web: fine membrane of skin connecting the digits of the foot; it stretches when the frog swims.

digit: terminal end of the limbs formed of various articulated bones; it has neither nails nor claws.

forelimb: short articulated member located behind the head; it has four digits and is used for walking.

lower eyelid: thin muscular membrane that is translucent and movable; it rises from the lower edge of the eye to protect and cleanse it.

mouth: anterior cavity of the digestive tract located on the ventral surface that allows food to be ingested.

nostril: external orifice of the nasal cavity located above the mouth and having olfactory and respiratory functions.

snout: anterior round protruding portion of the head that forms the mouth and the nostrils.

eyeball: protruding organ of sight contained in the bony cavity at the top of the head used to perceive light intensity, motion and shapes.

tympanum: thin strong elastic membrane connected to the inner ear to capture acoustic vibrations.

upper eyelid: thick fixed membrane.

trunk: bony portion of the body to which the head and limbs are attached.

Link for dissection video: http://youtu.be/FrDbIR-GU0k


Internal organs:

ring canal : circular canal where filtered water enters through the madreporite and flows into the radiated canals.

rectal cecum: waste is stored here before it goes through the anus.

stomach : receives food to be digested.

gonad : produces gametes (spermatozoids or ovules) depending on the sex of the starfish

pyloric cecum : radiated duct of the digestive tract produces digestive enzymes and allowed digested food to be stored.

gonopore :where gametes are expelled into the water to be fertilized.

intestine : where absorption of nutrients is carried out and waste is transformed into fecal matter.

radial canal : receives water from the annular canal, which then passed into the tube feet.

ampulla : contracts to let water enter the tube foot, allowing it to extend; when it dilates, the foot retracts.

esophagus : allows food to reach the stomach.

External organs:

Arms or rays - project from disc

Central disc - the center of the starfish 

Oral surface  - where the mouth is

Aboral surface - the top of the starfish

Madreporite - small white circular area, off-center on aboral surface of disc

anus - small centered aborally on disc, allows waste to be ejected

Spines - many short, rough, limy, in patterns over aboral surface

Eyespot - small, pigmented on one end of each arm

Ambulacral grooves - one along oral surface of each ray

Oral Spines - surround the mouth

Tube feet - soft, slender, with expanded tips; 2 or 4 rows in each groove

Mouth - on oral surface in center, allows food to be digested 

Link for dissection video: http://youtu.be/uh6MdVdMxe0






Monday, March 17, 2014

pGLO Lab

pGLO Lab


Genetic transformation is an alteration within genes that is a direct result of exogenous DNA. One can insert a specific gene into an organism in order to change its trait. In this lab, we transformed bacteria into a gene that codes for GFP, or Green Fluorescent Protein. This specific protein allows for a glowing of bright green under a ultraviolet light. In this experiment, the pGLO is resistant to the antibiotic ampicillin in the plasmid DNA. Transformed cells will only grow on the dishes with LB/amp and will not show on those without it 


The purpose of this pGLO lab was to insert a plasmid into the DNA of a bacteria. Dependent on the presence or absence of the sugar, arabinose, determined whether the bacteria glowed or not. We transformed this bacteria into a gene that codes for Green Fluorescent Protein. This protein is what makes the certain ecoli glow under the ultraviolet light.  We then compared the absence/presence of the pGlo and sugars.


First we had 2 test tubes, we labeled one +PGLO and the other one -PGLO. We also labeled the 4 LB agar plates. The first plate was LB/AMP/+PGLO. The second one was LB/AMP/ARA/+PGLO. The third plate was LB/AMP/-PGLO. The last plate was LB/-PGLO. AMP was the antibiotic and the ARA was sugar. Then we used a sterilized pipet and put 250 micro liters of transformation solution in both test tubes labeled PGLO + and -. Both tubes were then placed on ice. A single colony of bacteria put in the +PGLO. We do this by taking a sterile loop and putting it in the bacterial colony and the placing the sterile loop in the test tube. We swirl the loop in the tube to make sure the bacteria colony is completely immersed in the PGLO. This was repeated for -PGLO. Then we added a DNA plasmid in the +PGLO and not the -PGLO. We added the plasmid by using another sterile loop and taking the plasmid for a DNA stock tube, after we did that we swirled the loop in the +PGLO. Next we put both test tubes in a foam rake on ice for 10 minutes. After the 10 minutes we needed to heat shock the test tube. We did this by transfer the test tubes in the foam rake into a water bath that was 42 degrees Celsius for 50 seconds, and then putting the test tubes back on ice for 2 minutes. After the heat shock we used a sterile pipet to but 250 micro-liters of LB broth into both test tubes (+PGLO and -PGLO). The next thing we did was incubate the test tubes at room temperature for 10 minutes. We tapped the test tube with our fingers to make sure the LB was spreading out. Our next step was to pipet 100 micro liters of +PGLO  suspension to plate the nutrient plate 1 and 2. Then we pipeted 100 micro liters of -PGLO suspension  was added to plate 3 and 4. For each plate a new sterilized pipet was used. Next we used a sterile loop at spread the suspension around the plate. We did this by rubbing the loop all over the plate but we couldn't press too hard on the agar. We repeated this step for all 4 plates using new loops each time. We then flipped the plates upside down and stacked them to let the plates incubate in a 37 degree Celsius for the night. The next day we unflipped the plates to check the growth. Then we used a UV to check the plate LB/AMP/ARA/+PGLO to see if any of the bacteria were glowing. We took pictures of all the plates, to record the growth.


After letting the E.coli incubate over night, we were able to determine our results the next day. The Petrie dish with LB and -pGlo grew a big amount compared to all the other dishes. This happened because the dish only had LB (a type of broth) and -pGlo. This -pGlo did not have an effect on the cells. The bacteria grew like normal bacteria would. We made this dish even though we knew it would not glow in UV light to show that our bacteria did grow normally; it showed that the bacteria worked essentially. The next tray had LB/ AMP and -pGlo. This tray had the broth (LB) and an antibiotic (AMP). This tray did not experience any growth at all because it had the antibiotic and was missing the plasmid,+pGlo, which prevented it from growing. Another tray contained +pGlo, LB, and AMP. This had the broth and antibiotic as well as the plasmid, +pGlo. The dish grew approximately six colonies of DNA. It was able to grow because it had the antibiotic and plasmid. This tray did not glow in the UV light because it did not have the sugar, ARA, present that makes it glow. This dish acted as our control for the experiment. The last dish had the plasmid, +pGlo, the LB broth, the antibiotic, AMP, and lastly the sugar, ARA. The ARA sugar in this dish separated it from all the other ones. This tray glowed and grew about five colonies of bacteria. This tray glowed in the UV light because of the ARA sugar, plasmid, and antibiotic AMP. 
After seeing the growth in the different dishes, our group calculated the transformation efficiency of our experiment. The transformation efficiency is the extent to which we genetically transformed the bacteria (in this case, E.coli). When doing an experiment, of course, the more cells you genetically transform the better, so the higher the transformation efficiency the better as well. In this experiment's case, the transformation efficiency represents the total number of bacterial cells that express the green protein, divided by the amount of DNA used in the experiment. This then tells us the total number of bacterial cells transformed by one microgram of DNA. The formula used is: 

Transformation efficiency = total number of cells growing on the agar plate
                                             Amount of DNA spread on the agar plate 

Our transformation efficiency was 14.16 which is very off of the standard amount. Standard amounts are usually way higher, around about 8.0 x 10^2. Clearly, we did not genetically transform many of the DNA cells.  


From these results, we can come to two conclusions. E Coli can only grow in the presence of an anitbiotic when it has been treated with pGLO which causes the bacteria to become antibiotic resistant. The glowing characteristic of the pGLO, however, is only activated in the presence of a sugar. We know this is true because the bacteria only treated with pGLO and anitbiotic was able to grow but not glow but the bacteria treated with both grew and glowed.