1st Semester 40 - BIOLOGY JUNCTION

Scientific Equipment

Scientific Equipment All Materials © Cmassengale
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	Compound Light Microscope (LM)-used to enlarge an image		Graduated Cylinder – used to measure the volume of liquids
	Microscope Slide – supports an item being examined under the microscope		Cover slip – covers specimen on a slide
	Beaker – holds liquids while they are being stirred or heated		Test Tube Brush – used to clean test tubes
	Evaporating Dish – used for heating solids		Pinch Clamps – used to control the flow of liquids through tubing
	Funnel – assists in transferring liquids to containers with smaller openings		Striker – used to ignite a burner
	Test Tubes – holds liquids for observation or testing		Safety goggles – protects the eyes from damaging substances
	Pipet pump – dispenses known volumes of liquids		Eyedropper – used to transfer small amounts of liquids
	Forceps – used to hold or lift specimens		Magnifying glass – enlarges the image of an object
	Crucible – containers used for “strong” heating		Test Tube Rack – holds test tubes during observation or testing
	Wash Bottle – used for rinsing solids out of a container		Pipet – used for exact measurements of liquids
	Spatula – chemical spoons used to transfer solids from their original container to a scale for weighing		Wire Gauze – adds additional support for containers held on tripods or O-rings
	Crucible Tongs – used for picking up crucibles & crucible covers only		Mortar & Pestle – used to grind solids into powders
	Florence Flask – used to store liquids		Erlenmeyer Flask -used to store solutions
	Dissecting Pan – holds specimen being dissected		Test Tube Holder – holds test tubes while heating
	Electronic Balance – used for weighing substances		Bunsen Burner – heat source
	Thermometer – used to measure temperature	Stopper – used to cap flasks containing liquids
	Scalpel – used for cutting specimens being dissected		Tubing – hose used for connecting glassware
	Petri Dish – plate used to culture microorganisms		Triple Beam Balance – used for weighing substances
	O-Ring – used with ring stands to support heated vessels		Volumetric Flask – used to mix precise volumes of liquids
	Watch Glass – used on top of beakers when heating	Desiccators – used to remove moisture from substances
PRINT EQUIPMENT SHEET FOR NOTEBOOK		BACK

Scientific Method
All Materials © CmassengaleHow can we determine if something is a fact or an opinion? How can we determine an answer to a problem? The answer is use the scientific method.What is the Scientific Method? It is a series of steps used to help solve a problem.

Step 1. Make an Observation. After making an observation of the natural world, define the problem and make sure only one problem is being studied. ALL scientific experimentation starts with observation.
Step 2. Research the problem (question). Use all available resources to collect data on the subject being covered. Libraries, Internet, books, magazines, personal interviews, etc.
Step 3. Develop a hypothesis (educated guess). Make it a short definitive statement. It may be an “if” then” statement. The “if” part will become the hypothesis and the then part should be the results received at the end of the controlled experiment. Remember your hypothesis can be changed if the results do not support it.
Step 4. Develop a controlled experiment. A controlled experiment is an experiment that contains only one experimental variable. An experimental or independent variable is the thing being tested (what the scientist changes). Everything else in the experiment or all other variables must be the same. These variables are also called the controlled variables. Keeping these variables the same allows the experimenter to show that it was the experimental variable that caused the results. The dependent variable is what changes when the independent variable changes – the dependent variable depends on the outcome of the independent variable. Data should be organized into charts, tables, or graphs.
Step 5. Analyze the data and come up with a conclusion. Data may be quantitative (numbers) or qualitative (appearance, properties, etc.). The conclusion may or may not support the hypothesis. Additional experimentation must then take place to build documentation concerning the problem. If the hypothesis is proven wrong, change the hypothesis, not the data. Scientists must be unbiased.
WHAT FOLLOWS: Scientific research must be published, but first it must be reviewed by peers (other scientists) and verified for accuracy. Research may result in a scientific theory or law.

Example:

Observation:	Toaster stops working.
Question/Research:	What is wrong with the toaster? (Read toaster Manual.)
Hypotheses:	(1) It is unplugged. (2) The unit is burned out.
Experiments:	(1) Check the plug. (2) Take the toaster apart and look at the heating wires.
Results & Conclusion:	If it was unplugged the first hypothesis is supported, if the wires inside are broken, then the second hypothesis is supported.

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RNA interference abstract

RNA Interference – Gene Silencing by Double-Stranded RNA
Andrew Z. Fire & Craig C. Mello
Nobel Prize Award in Medicine 2006

Introduction

This year’s Nobel Laureates have discovered a fundamental mechanism for controlling the flow of genetic information. Our genome operates by sending instructions for the manufacture of proteins from DNA in the nucleus of the cell to the protein synthesizing machinery in the cytoplasm. These instructions are conveyed by messenger RNA (mRNA). In 1998, the American scientists Andrew Fire and Craig Mello published their discovery of a mechanism that can degrade mRNA from a specific gene. This mechanism, RNA interference, is activated when RNA molecules occur as double-stranded pairs in the cell. Double-stranded RNA activates biochemical machinery which degrades those mRNA molecules that carry a genetic code identical to that of the double-stranded RNA. When such mRNA molecules disappear, the corresponding gene is silenced and no protein of the encoded type is made.

RNA interference occurs in plants, animals, and humans. It is of great importance for the regulation of gene expression, participates in defense against viral infections, and keeps jumping genes under control. RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future.

The flow of information in the cell: from DNA via mRNA to protein

The genetic code in DNA determines how proteins are built. The instructions contained in the DNA are copied to mRNA and subsequently used to synthesize proteins (Fig 1). This flow of genetic information from DNA via mRNA to protein has been termed the central dogma of molecular biology by the British Nobel Laureate Francis Crick. Proteins are involved in all processes of life, for instance as enzymes digesting our food, receptors receiving signals in the brain, and as antibodies defending us against bacteria.

Our genome consists of approximately 30,000 genes. However, only a fraction of them are used in each cell. Which genes are expressed (i.e. govern the synthesis of new proteins) is controlled by the machinery that copies DNA to mRNA in a process called transcription. It, in turn, can be modulated by various factors. The fundamental principles for the regulation of gene expression were identified more than 40 years ago by the French Nobel Laureates François Jacob and Jacques Monod. Today, we know that similar principles operate throughout evolution, from bacteria to humans. They also form the basis for gene technology, in which a DNA sequence is introduced into a cell to produce new protein.

Around 1990, molecular biologists obtained a number of unexpected results that were difficult to explain. The most striking effects were observed by plant biologists who were trying to increase the colour intensity of the petals in petunias by introducing a gene inducing the formation of red pigment in the flowers. But instead of intensifying the colour, this treatment led to a complete loss of colour and the petals turned white! The mechanism causing these effects remained enigmatic until Fire and Mello made the discovery for which they receive this year’s Nobel Prize.

The discovery of RNA interference

Andrew Fire and Craig Mello were investigating how gene expression is regulated in the nematode worm Caenorhabditis elegans (Fig. 2). Injecting mRNA molecules encoding a muscle protein led to no changes in the behaviour of the worms. The genetic code in mRNA is described as being the ‘sense’ sequence, and injecting ‘antisense’ RNA, which can pair with the mRNA, also had no effect. But when Fire and Mello injected sense and antisense RNA together, they observed that the worms displayed peculiar, twitching movements. Similar movements were seen in worms that completely lacked a functioning gene for the muscle protein. What had happened?

When sense and antisense RNA molecules meet, they bind to each other and form double-stranded RNA. Could it be that such a double-stranded RNA molecule silences the gene carrying the same code as this particular RNA? Fire and Mello tested this hypothesis by injecting double-stranded RNA molecules containing the genetic codes for several other worm proteins. In every experiment, injection of double-stranded RNA carrying a genetic code led to silencing of the gene containing that particular code. The protein encoded by that gene was no longer formed.

After a series of simple but elegant experiments, Fire and Mello deduced that double-stranded RNA can silence genes, that this RNA interference is specific for the gene whose code matches that of the injected RNA molecule, and that RNA interference can spread between cells and even be inherited. It was enough to inject tiny amounts of double-stranded RNA to achieve an effect, and Fire and Mello therefore proposed that RNA interference (now commonly abbreviated to RNAi) is a catalytic process.

Fire and Mello published their findings in the journal Nature on February 19, 1998. Their discovery clarified many confusing and contradictory experimental observations and revealed a natural mechanism for controlling the flow of genetic information. This heralded the start of a new research field.

The RNA interference machinery is unraveled

The components of the RNAi machinery were identified during the following years (Fig 3). Double-stranded RNA binds to a protein complex, Dicer, which cleaves it into fragments. Another protein complex, RISC, binds these fragments. One of the RNA strands is eliminated but the other remains bound to the RISC complex and serves as a probe to detect mRNA molecules. When an mRNA molecule can pair with the RNA fragment on RISC, it is bound to the RISC complex, cleaved and degraded. The gene served by this particular mRNA has been silenced.

RNA interference – a defense against viruses and jumping genes

RNA interference is important in the defense against viruses, particularly in lower organisms. Many viruses have a genetic code that contains double-stranded RNA. When such a virus infects a cell, it injects its RNA molecule, which immediately binds to Dicer (Fig 4A). The RISC complex is activated, viral RNA is degraded, and the cell survives the infection. In addition to this defense, higher organisms such as man have developed an efficient immune defense involving antibodies, killer cells, and interferons.

Jumping genes, also known as transposons, are DNA sequences that can move around in the genome. They are present in all organisms and can cause damage if they end up in the wrong place. Many transposons operate by copying their DNA to RNA, which is then reverse-transcribed back to DNA and inserted at another site in the genome. Part of this RNA molecule is often double-stranded and can be targeted by RNA interference. In this way, RNA interference protects the genome against transposons.

RNA interference regulates gene expression

RNA interference is used to regulate gene expression in the cells of humans as well as worms (Fig 4B). Hundreds of genes in our genome encode small RNA molecules called microRNAs. They contain pieces of the code of other genes. Such a microRNA molecule can form a double-stranded structure and activate the RNA interference machinery to block protein synthesis. The expression of that particular gene is silenced. We now understand that genetic regulation by microRNAs plays an important role in the development of the organism and the control of cellular functions.

New opportunities in biomedical research, gene technology and health care

RNA interference opens up exciting possibilities for use in gene technology. Double-stranded RNA molecules have been designed to activate the silencing of specific genes in humans, animals or plants (Fig 4C). Such silencing RNA molecules are introduced into the cell and activate the RNA interference machinery to break down mRNA with an identical code.

This method has already become an important research tool in biology and biomedicine. In the future, it is hoped that it will be used in many disciplines including clinical medicine and agriculture. Several recent publications show successful gene silencing in human cells and experimental animals. For instance, a gene causing high blood cholesterol levels was recently shown to be silenced by treating animals with silencing RNA. Plans are underway to develop silencing RNA as a treatment for virus infections, cardiovascular diseases, cancer, endocrine disorders and several other conditions.

Reference:
Fire A., Xu S.Q., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-811.

Andrew Z. Fire, born 1959, US citizen, PhD in Biology 1983, Massachusetts Institute of Technology, Cambridge, MA, USA. Professor of Pathology and Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Craig C. Mello, born 1960, US citizen, PhD in Biology 1990, Harvard University, Boston, MA, USA. Professor of Molecular Medicine and Howard Hughes Medical Institute Investigator, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.

High resolution image (pdf 2,5 Mb) »

Sample 1 Bioremediation

Lab: Oil Degrading Process

Introduction:
Oil spills are very hazardous to the environment and wildlife. Photographs of oil drenched birds and various sea animals are all in the back of our minds. Oil spills have become a greater problem as off shore drilling takes place. Studies show that about 5-10 million tons of oil is spilled every year. There are several sources for these oil spills and they include: cargo tanker spills at sea, waste oil pumping at sea, in port oil losses, and tanker accidents.

Cargo tanker washings at sea take place when the tankers use seawater as ballast to stabilize the craft after they have discharged their oil. This oil-contaminated water is then discharged back onto the ocean when the tanker is refilled. Waste oil pumping at sea takes place when dumping by ships other than tankers contributes an estimated 500,000 tons of oil annually. In port oil losses are attributed to collisions in ports and to procedures during loading and unloading of oil. This adds about 1 million tons of oil to sea pollution. Tanker accidents on the high seas or near the shore recently have added to the problem and have received great amounts of public attention. The Exxon Valdez the largest oil spill in history was carrying 1.2 million barrels of oil when in it ran into a reef off the coast of Alaska. Exploration losses occur during the search for and production of oil due to blowout of wells and accidental damage due to offshore drilling platforms. Oil can also leak form the 200,000 miles of pipeline that crosses waterways from cracks, punctures or corrosion in the pipes.

Two million barrels of motor oil are estimated to be lost every tear. Much of this oil ends up in coastal waters and shores. When one gallon of oil spilled in the ocean it can spread out for four acres. However 25% of spilled away is lost through evaporation. The remaining oil causes large amounts of oil to the marine life in the area that it was spilled. This oil will form a highly viscous material that sticks to every thing as it finds it way to the sea floor including: bird, fish, and marine mammals. Microorganisms and photo oxidation will break down the oil that does not this thick sticky substance. However oil spills that take place near shore have many different effects because the oil does not have enough time to break down. This causes many animals and much of the coastline to be covered with a very sticky black layer of oil.

When oil is spilled the short-term effects of the spill receive the most attention. The light intensity below an oil slick can be reduced by 90%. Oil films slow the amount of oxygen that is taken up by water. Polluted water has lower dissolved oxygen level than clean water. Birds that rely on the ocean for their survival are often greatly affected by spills. When oil forms a coat around the bird’s feathers it reduces the bird’s ability to fly, float and reduces the bird’s insulation ability. This causes many birds to doe from the cold, or their capability to get food. Compounds in oil such as benzene, toluene, xylene, naphthalene, and phenanthrene are toxic to man and animals. As a result many marine animals are killed as a result of an oil spill.

The long-term effects of an oil spill are not as easily seen as the short term effects. After oil has been in the water for a period of time it begins to affect many chemical messengers that animals rely on to survive such as finding food or escaping from predators. Oil is also incorporated into the animals’ body, as it becomes a part of the environment. Some marine animals that humans eat have fractions of oil in them, which can serve as a growing medium for many poisons.

Many methods have been developed to clean up oil spills. Skimmers are used to remove oil from the surface of the water. Skimmers work by skimming a thin of water and oil form the surface. Booms are used to contain the oil before it is skimmed. Clay, sawdust, straw, chopped corn and other absorbents have used to absorb spilled oil. Solvents have also been used to break the oil down. Burning the oil has even been attempted but it fails to completely break the oil down and makes a toxic smoke that contains carcinogenic compounds.

Oil is composed of many compounds that contain many hydrocarbons. The hydrocarbons of oil are broken down by fractional distillation. Since each compound of oil has different boiling points the compounds can be separated and collected by boiling the oil. Gasoline is distilled from below twenty degrees Celsius. Petroleum ether is separated from oil between twenty and sixty degrees. Ligroin is removed from the oil between sixty and one hundred degrees. Kerosene is removed form oil between 175 and 325 degrees. Many of these carbon compounds are cyclic compounds, which mean their atoms are attached to form rings.

In recent oil spills it has been learned that mechanically cleaning up the spill can be very complex, ineffective, and expensive. Mechanically cleaning up a spill depends upon the equipment available, workers and available, and normally it can only recover 10%-30% of the oil.

Biologically cleaning up oil spills is a great alternative to mechanical cleanup. Using microorganisms to clean up a spill is environmentally friendly and allows more of the spill to be cleaned up. This process involves seeding the oil spill with oil hungry microorganisms, bacteria yeasts, and fungi, and fertilizer to brake the oil down into masses of food and nontoxic cells that are absorbed into the food chain. These marine microorganisms naturally depend on hydrocarbons for survival so this is a natural alternative to mechanical methods. Fertilizers are spread out over the spill to promote the microorganism’s growth. Within days of when the organisms were applied to the spill changes in the oil can be seen. The oil noticeably is beginning to be broken down into fragments and other compounds. The remaining oil fractions become intermixed with and consumed by high forms of marine life.

This must all take place aerobically in the presence of oxygen. This explains why oil is able to be unchanged while it is underground. When oil is biologically broken down it products are acetate units, which are oxidized to carbon dioxide through the Krebs Cycle.

An aliphatic hydrocarbon is a compound that consists of carbon atoms joined together to form an open chain. Aliphatic compounds are oxidized into a two-carbon molecule, acetyl CoA that is catalyzed by a monooxygenase. The initial step of the oxidation of aliphatic hydrocarbons requires oxygen to serve as a reactant. The oxygen molecule is incorporated into the oxidized hydrocarbons and monoxygeneses are generally involved.

Investigation 1
Hypothesis:
In this investigation the bacteria Pseudomonas and the fungi Penicillium will break down the refined oil in the test tubes. The Pseudomonas species will brake the oil down more than the Penicillium species causing the water in test tube one to have a higher turbidity.

Materials:
The materials used in this investigation are as follows: 2 test tubes with caps, 60 mL of distilled water, one density test indicator strip, one test tube rack, Pseudomonas species culture, Penicillium species culture, a syringe, two 1 mL pipettes, and refined oil.

Procedure:
Begin by obtaining two tubes and labeling them tube # 1 pseudomonas, and tube #2 Penicillium. Add approximately 5 mL of distilled water to each tube. Next, place 4-5 drops of the refined oil to each test tube. Make sure to take notes of the general appearance of the color and texture of the oil. Record thee results from tube one in table one under day 0. Record the results from tube two in table two under day zero. Next, team member one in the group needs to inoculate tube one with the Pseudomonas, while team member two inoculates tube two with the Penicillium species. Do this by using a sterile pipette to add .5 mL of the assigned culture to the right tube. After completing this screw the cap on each tube tightly and invert the tube several times to mix; this mimics the wave action that would occur in the ocean. Then, place the tubes in an incubator set at thirty degrees Celsius for twenty-four hours. Make sure the cap on each tube is loosened one half turn. Make sure to invert the tubes once daily to increase the dissolved oxygen concentration in each tube. Also observe the tubes ever twenty-four hours for 3-4 days and make careful observations of the general appearance and characteristics of the oil. Also using an indicator measure the turbidity of the water in the tube every day. Record the results from tube one in table one and the results form tube two in table two.

Results:

Observations: Pseudomonas Species Application
Table 1

	General Appearance Characteristic of oil	Color of oil	Turbidity of water
Day 0	The oil forms a thin uniform layer across the surface of the	Amber	0
Day 1	The oil is lighter in color and has begun to brake into tiny fragments. There is a clear ring in the middle	Light Yellow	0
Day 2	The oil has broken down significantly. It is fragmented and is cloudy in appearance	Cloudy with a hint of yellow	0
Day 3	The oil is almost gone. A small ring is around the edge of the tube.	Murky yellow ring	0
Day 4	The oil can be barely seen in very small fragments	Clearish coudy	0

Observations: Penicillium Species Application
Table 2

	General Characteristics of oil	Color of oil	Turbidity of water
Day 0	The oil forms a thin uniform layer over the surface of the water.	Amber	0
Day1	Oil has become lighter in color. The oil appears to becoming frothier in nature.	Light yellow	0
Day 2	The oil is fragmenting. A white cloudy ring has formed. A growth has developed on the sides of the tube.	Whitish cloudy with a yellow hue	0
Day 3	The oil has fragmented and broken down significantly. The ring now only is along the edge of the tube.	Cloudy whitish yellow	0
Day 4	Oil is not detectable. Colonies fading.	Not available	0

Describe the physical characteristics and appearance of oil on day 0.
The oil on day 0 was amber yellow in color. The oil formed a thin uniform layer over the surface of the water.

Describe any changes in the physical characteristics and appearance of the oil on Day 1 and beyond, and discuss causes for such changes.

On day 1 the oil became a light yellow. On day two the oil had began to fragment and was a more whitish color. On day three the oil broken down more into more droplike fragments. A faint ring formed around the edge of the tube. On day 4 the oil was completely broken down.

Is there a difference in the rate of oil degradation between the bacterial and fungal culture?

Yes the fungal culture slightly broke the oil down quicker.

What does turbidity indicate?

Turbidity indicates the amount of oil being broken down and becoming part of the water.

What is the turbidity level of your culture after 4 days of incubation? How long do you think your culture will continue to grow?

The turbidity was 0. I believe the culture will continue to grow for a day or two at the most because the oil is almost completely degraded.

What is the limiting growth factor in your test tubes?

The amount of oil and the lack of space in the test tube.

Research the nutritional requirements and environmental conditions that promote the growth of bacteria and fungi. Suggest optimum conditions to culture bacteria and fungi.

Bacteria and fungi grow the best in a warm damp environment.

Investigation 2
Hypothesis:
The fertilizer in the jars and the amount of space in the jars will promote more bacterial and fungal growth causing the oil to broken down quicker than in the tubes. The Pseudomonas species will brake the oil down faster than the Penicillium species.

Materials:
The materials needed for this investigation are 2 clear plastic jars with screw caps, 400 mL of distilled water, a density indicator strip, 2 grams of nutrient fertilizer, a sterile pipette, Pseudomonas species bacteria, and Penicillium species fungi.

Procedure:
Begin the investigation by pre-labeling the jars #1 Pseudomonas species, and jar 2 Penicillium species. Next, fill the jars half full with water. Using a pipette add 15-20 drops of oil, to form a thin layer in order to simulate an oil spill. Make sure to make an initial observation of the general appearance and characteristics of the oil and record the results from jar one in table 3 and the results from jar two in table 4. Then, using your fingers sprinkle a fine layer of fertilizer over the entire layer of oil. Using another pipette inoculate jar # 1 with 1.25 mL of Pseudomonas species medium and jar # 2 with 1.25 mL of Penicillium species liquid medium. Place the jars in an incubator set at thirty degrees Celsius and make sure the lids on the jars are loose to let oxygen in. Make sure to observe the jars once every 24 hours for 4 days. Record your observations in tables 3 and 4. Using a pipette, once a day blow bubbles into the liquid in the jars to increase oxygen content in the water.

Results

Observations: Pseudomonas Species Application
Table 3

	General appearance characteristics of oil	Color of oil	Turbidity of water
Day 0	Oil forms a thin uniform layer over the surface of the water.	Amber	0
Day 1	The oil remains mostly the same except for a few beads in the middle.	Goldish amber	0
Day 2	The oil is swirly. It is braking up into a very few new fragments.	Cloudy whitish in color	4
Day 3	The oil is more beaded and does not cover as much of the water.	Whitish cloudy	5
Day 4	The oil has broken up into very small traces. The colonies are larger and noticeable.	Cloudy/ Clear	5

Observations: Penicillium Species Application
Table 4

	Characteristics appearance of oil	Color of Oil	Turbidity
Day 0	Oil forms a thin uniform layer over the water	Amber	0
Day 1	Oil now is swirly and cloudy	Goldish Yellow	0
Day 2	Swirly, beady and breaking up, not covering all the water	Cloudy white	0
Day 3	Broken down more and beady, whitish blob formed in middle	Whitish	0
Day 4	Beaded more but oil still remains	Whitish	0

Describe what happens to the oil after several days of microbial degradation. Are the microbes breaking up the oil? Can you detect an increase in microbial growth?

After several days the oil has broken into many fragments and does not completely cover the surface of the water. Yes the microbes are braking up the oil. Yes I can detect an increase in microbial growth.

Is the oil over the surface completely degraded? Can you still see any remaining oil on the surface? If so, explain.

Yes, a light swirl of oil remains over the top of the water. The swirl is cloudy white. This oil still has not been completely broken down.

What happens to oil when it is biologically degraded in the ocean?

It is broken down and absorbed by the water, the bacteria, and other marine animals. This causes it to become part of the natural environment.

What is the purpose of the nutrient fertilizer used over the oil spill?

The fertilizer speeds up the growth of the bacteria and fungus. The bacteria and fungi are the in turn able to degrade more oil.

Are there any adverse effects of using fertilizer over an actual oil spill to enhance indigenous microbial growth?

Yes fertilizer can pollute the water and can cause harmful effects to marine and plant life in the ocean.

Did you observe an increase in turbidity over time? Which of the two simulations was more turbid? Explain.

Yes there was an increase in turbidity over time. The jar containing the Pseudomonas species of bacteria was more turbid. The oil in this jar had been broken down more causing the water to be darker.

Did you observe fungal and bacterial growth in the test tubes or jars? Explain.

The jars had more fungal growth because a larger amount of oil was degraded due to the jars excess space and the nutrient fertilizer used.

Based on the information provided, do you think that the microorganisms would be effected by water temperature? Would they follow the floating oil or be dissipated by shifting winds or currents? And if they did eat the oil, would the residue damage marine life?

Yes water temperatures could affect the microorganisms. The organisms would follow the oil. Finally, no the oil residue would not damage any marine life.

Based on the physical characteristics of oil and water discuss possible resulting problems associated with oil spills.

Since oil does not mix with water the oil forms a thick sledge on top of the water that sunlight can not penetrate. This harms the many plants near the spill that depend on sunlight to carry out photosynthesis. The thick oil also gets into birds feathers that can prevent a bird from flying and insulating itself. Fish can also get the thick sludge on them affecting their gills.

In this investigation, we evaluated the ability of microbes to degrade oil under optimum conditions. Based on your findings, discuss possible environmental limitations in using such a method over an actual oil spill in the ocean.

Possible environmental limitations that could prevent this technique form being used is temperature which effects the growth of the bacteria and fungus. Shifting of bacteria by waves can also propose a threat. The natural occurrence of oil becoming thicker and sinking to the ocean floor also proposes a problem.

If you had to describe which clean up method to use in actual oil spill, would you use such a bioremediation method or use a mechanical method described in the introduction? Explain your decision.

I would use biological remediation because it is able to clean up more of the oil, is possibly cheaper, and is more environmentally friendly.

Assuming that you need 10-6 lbs. of highly concentrated cell mass mixed with nutrient fertilizer for the degradation of oil covering 0.022 sq. ft, as in the simulated oil spill, estimate the amount of cell mass and fertilizer mixture in pounds that would be needed to degrade the oil covering 1 square mile of an ocean. Assume there is the same amount of oil relative to the area.

Investigation 3
Hypothesis:
The bacteria and fungus will brake down the oil in the dish but not as well as the previous two because of the sand interfering with the degradation.

Materials:
The materials used in this investigation are 2 petri dishes, 60 mL distilled water, 2 grams of nutrient fertilizer, Pseudomonas and Penicillium cultures, and a sterile pipette.

Procedure:
Begin by pre-labeling two petri dishes #1 Pseudomonas and #2 Penicillium. Then, remove the lids and line each of the petri plates with a layer of sand. Make sure to spread the sand evenly over the plate. Next to simulate the shore conditions moisten the sand with distilled water until a thin layer of residual layer of water forms over the sand. Add 15-20 drops of refined oil throughout the surface, enough to form a thin layer to simulate an oil spill. Allow the oil to spread over the whole surface. Make initial observations of the condition of the oil and place results in tables five and six. Then using your thumb, sprinkle a fine layer of fertilizer over the oil. Using the pipette add 1.25 mL of the Pseudomonas culture to dish one and 1.25 mL of the Penicillium culture to dish 2. Place the lids on the dishes and store them in an incubator set at thirty degrees Celsius. Finally once a day for four days make observations of the oil.

Results

Observations: Pseudomonas Species Application
Table Five

	General Appearance characteristics of oil	Color of oil	Turbidity of water
Day 0	Oil spread evenly over the surface of the sand and water creating a uniform layer	Amber	0
Day 1	Oil remains similar darker in some parts than others	Golden yellow	0
Day 2	Oil clear and yellow tanish parts have tiny beads	Yellow	0
Day 3	Broken down a little more than day 3 into a few more beads	Yellow	0
Day 4	Not available.	N/A	N/A

Observations: Species Penicillium Species Application
Table Six

	General Characteristics of oil	Color of oil	Turbidity
Day 0	Oil spreads out over the surface of the water forming a thin uniform layer	Amber	0
Day 1	Oil remains similar, but darker in some places than others	Amber	0
Day 2	Oil amounts have decreased. Some may soaked into sand.	Yellow	1
Day 3	The oil not detectable. A dime size black spot in the center of dish identified as mold	N/A	N/A
Day 4	Oil characteristics N/A. Large black colony of fungus growing in the middle of container	N/A	N/A

Describe the physical and chemical changes of the oil after several days of microbial degradation.

Day 1 the is darker in some parts than others. Day 2 oil is tanish and has no beads. Day 3 the oil in parts is beady. On day 4 the oil had disappeared probably sinking into the sand.

How effective do you think such a method is when in an actual oil spill on the shore? What happens to the degraded oil and the resultant microbial mass?

This method is less effective than it is in the open ocean because the oil can soak into the sand, but it is more effective than mechanical methods. The degraded oil and microbial mass either stay in the sand or are washed out to sea.

Discuss the limitations of using a mechanical method to clean up a spill on the shore. What are the limitations of using a remediation method? Which of the two methods would be the most efficient and economical to clean up oil spills.

For the mechanical methods the water has to be smooth and still. For the remediation the bacteria do not grow as well in the sand. The remediation is more effective and economical than mechanical methods.

Discuss the effect of an oil spill on the shore would have on plant life along the shoreline protists, and other larger animals.

The oil could get on the plants preventing them from absorbing sunlight. The oil could poison protists or get on them and prevent them from moving. Larger animals could get oil in their fur and prevent them form insulating themselves. It could prevent birds form both flying and insulating themselves.

In the Alaskan oil spill chemical detergents wee not used. Why? Explain the use of detergents.

Detergents weren’t to because of the cold temperatures. Detergents are used to help break the oil down by making water a better solvent. Detergents work the best in warm water.

Discuss the potential of bioremediation procedures in detoxifying the air, water, soil, and waste materials.

In the same way it is used in an oil spill bioremediation can be used to break down harmful waste products such as sewage. Factories could use remediation to clean the air before emitting it into the environment. When an hazardous chemicals pollute the soil remediation could be used to make the soil safer. Water could be treated with bioremediation after it is used and before it is pumped into streams, rivers, and oceans.

What can be done to prevent oil spills.

Better training tanker ship captains to avoid running into obstacles that could rip into the tanker. Keeping better maintenance on the pipelines that are used to transport oil. Being careful to prevent the leakage of motor oil from cars and other machines.

How are we affected by oil spills? Discuss the physical and economic consequences of oil spills.

Oil spills prevent from enjoying the marine life of the ocean, beaches, and the ocean itself. Fish we eat can be contaminated with oil compounds. Oil spills require a lot of money to clean up so normal people usually carry this burden.

Research other energy sources that can be used to cut our dependence on oil.

The use of electric cars could lower our dependence of oil. The development of hydrogen powered fuel cell that uses water for energy could also cut our dependence on oil. Using solar power could also cut our dependence on oil.

Error Analysis:
In investigation one not properly inverting the tubes every day could have caused the results received to be inaccurate. In investigation two not evenly spreading the fertilizer completely over the oil could have caused certain regions to have more growth than others causing false results. On investigation three using the slant to attain the Pseudomonas and Penicillium instead of the liquid culture may have caused false results.

Conclusion:
Using bioremediation is clearly a great alternative that is more cost effective, environmentally friendly, and productive than mechanical methods to clean up an oil spill. Bioremediation works best when mixed with a fertilizer to promote microorganism growth and spread over the open water. When bioremediation is used on coastal areas it productivity is reduced because the oil can sink into the sand and into the ground. When used without fertilizer in the open water bioremediation is not as effective because the microorganism growth is not enhanced. All in all bioremediation is very effective in cleaning up an oil spill.

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Scientific Method & Genetics

Using the Scientific Method With Genetics

Introduction:

Humans are classified as a separate species because of all the special characteristics that they possess. These characteristics are controlled by strands of DNA located deep inside their cells. This DNA contains the code for every protein that an organism has the ability to produce. These proteins combine with other chemicals, within the body, to produce the cells, tissues, organs, organ systems, and finally the organism itself. The appearance of these organs, such as the shape of ones nose, length of the fingers, or the color of the eyes is called the phenotype.

Even though humans contain hands with five fingers, two ears, or one nose, there are subtle differences that separate these organs from another. There are subtle differences in a person’s genes that allows for these different phenotypes. In this lab, we are going to observe some of these differences in phenotype. All human hands look pretty much alike, but there are genes on your chromosomes that code for the characteristics making up your hand. We are going to examine two of these characteristics (hand width and hand length) and try to determine why these phenotypic differences occurred.

Materials:

metric ruler (see end of lab)
pencil
calculator

Procedures:

Day 1

Choose a partner and have them measure the length of your right hand in centimeters. (Measure from the tip of your middle finger to the beginning of your wrist as shown in figure 1.) Record your measurements in Table 1.
Now measure and record the length in centimeters of your partners hand.
Have your partner measure the width of your right hand, straight across the palm, and record the data in Table 1. (see figure 1.)
Now measure & record the width of your partner’s hand.

Figure 1.

Table 1

Group Data on Right Hand Width and Length
Student Name	Length of Hand (cm)	Width of Palm (cm)

After the entire class has completed Table 1, record your group data on the Class Data Table at the front of the room
Record the Class Data Table information on your lab sheet’s Table 2.

Table 2

Class Data on Right hand Width and Length (cm)
Class Period:
Student	Gender (M / F)	Hand Length (cm)	Hand Width (cm)
1.	M / F
2.	M / F
3.	M / F
4.	M / F
5.	M / F
6.	M / F
7.	M / F
8.	M / F
9.	M / F
10.	M / F
11.	M / F
12.	M / F
13.	M / F
14.	M / F
15.	M / F
16.	M / F
17.	M / F
18.	M / F
19.	M / F
20.	M / F
21.	M / F
22.	M / F
23.	M / F
24.	M / F

Click for Class Data Table

Day 2

In order to form a more accurate conclusion, the collection of additional data from several classes is necessary. Using the Class Data Tables for each period at the front of the room, record the # of males and # of females having the same length hand in Table 3.
Only record a hand length (e.g. 18.1 cm) once on table 3.

Table 3:

Hand Length (cm) of All Class Periods
Measurement of Hand length (cm)	# of Males	# of Females	Total # (Male + Female)

Using the Class Data Tables for each period at the front of the room, record the # of males and # of females having the palm width in Table 4.
Only record a palm width (e.g. 15.3 cm) once on table 4.

Table 4:

Hand Width (cm) of All Class Periods
Measurement of palm width (cm)	# of Males	# of Females	Total # (Male + Female)

Line graph data from table 3 using hand length as your independent variable and the number of times (total males & females) that measurement appeared as the dependent variable.
Make a second line graph using data from table 4 using palm length as your independent variable and the number of times (total males & females) that measurement appeared as the dependent variable.
Be sure to include a title for each graph and label the x and y axis and include their unit of measurement.

Graph Title: ___________________________________________________________

Analysis:

1. Examine the above graphs. What is the shape of the line for hand length? for the palm width?

2. What is the most abundant measurement (mode) for hand length?

3. What was the average hand length (mean) for males? for females? for total students?

4. What is (are) the least abundant measurement(s) for hand length?

5. What is the most abundant measurement (mode) for palm width?

6. What is the least abundant measurement for palm width?

7. What was the average palm width (mean) for males? for females? for total students?

8. Are there any similarities in the graph of the above two characteristics and if so, what are they?

9. Are there any differences in the graph of the above two characteristics and if so, what are they?

10. Is there a difference in the length of the male and female hand?

11. Is there a difference in the width of the male and female hand?

12. Does gender have an effect on the phenotype of a trait? Explain.

Cut and use:

Category: 1st Semester