Biology Exam 5

the phenotypic ratio- details

# of dominant phenotype offspring: # of recessive phenotype offspring.Since all F1 offspring are identical (Tt -Tall) one might, incorrectly assume, that the parent plants can only produce 1 offspring. In truth the parent plants (TT x tt) can produce hundreds of individual offspring, but can only produce 1 type of offspring, heterozygous tall (Tt) offspring.To find the F2 phenotypic ratio two F1 individuals are mated; in the case of pea plants, we allow the F1 individuals to self-pollinate which is the same as mating two F1 individuals. This cross is set up following the same procedure used for the P generation, except F1individuals are the parents: F1-Generation: Parent 1, Parent 2 Phenotype: Tall Tall Genotype: Tt Tt Gametes: T and t T and t

3 steps of PCR

, once the reaction solution has been prepared. One cycle consists of all three steps; 30-45 cycles are typically run on each sample. 1. Denaturation -This occurs at 95 oC and is used to disrupt the hydrogen bonds holding the two strands of the template DNA together. This cycle lasts 30-45 seconds. 2. Annealing -Occurs at 50-65 oC, depending on the sequence of the primers used. At the target temperature the primers will bind to the complementary sequence on the template DNA strands. This cycle lasts 30-60 seconds. 3. Synthesis -During this step, the temperature is raised to 72 C, the optimal temperature for Taq Polymerase activity. TaqPolymerase molecules bind to annealed primer sequences and use dNTPs to assemble the complementary strand. This stage lasts for 1-2 minutes. The length of the new strand is limited by the quality of the Taq polymerase; 1,000-4,000 nucleotides may be added in a single cycle.The three steps are completed in a PCR machine (also called a thermal cycler) that raises and lowers the temperature following a user-provided program.

rules for punnett squares

-Each parent should be written out with its phenotype, genotype and the gametes they can produce• -The gametes from one parent are written on the left side and the other parent along the top of the Punnett square, it doesn't matter which parent is in which positionThe Law of Segregation tells us that each individual carries 2 factors but passes only 1 factor in a gamete. Since the plants are homozygous, they can only form one type of gamete. To determine the possible gametes an individual can produce in a one-trait cross simply separate the two alleles of the genotype, each letter/allele goes into a gamete. ex. Let's start with a one-trait cross: A tall, true-breeding pea plant is mated with a short plant, find the F1 and F2 phenotypic ratios.The information given is for the P-generation while the final answers, the phenotypic ratios, are for the two subsequent generations. In the P-generation both parents are homozygous; this is known because the problem states that the tall plant is true-breeding, which means homozygous. The short plant expresses the recessive trait and the only way that can happen is if it carries two short alleles, so we know it is homozygous recessive. We are ready to set up our Punnett square now.P-Generation: Parent 1 Parent 2, Phenotype: Tall/Short Genotype: TT tt (you can use any letter you like) Gametes: T t

Seven pea characteristics

-flower color -flower position -seed color -seed shape -pod color -seed length. mendel collected data regarding these seven traits of peas. The ratio of dominant to recessive characteristics demonstrated a 3:1 ratio. Note that the left column of characteristics are the dominant characteristics while the right column are the recessive characteristics. Applying his mathematical and statistical background helped Mendel understand the ratios of plants he counted. Notice that the F2 ratios for all 7 characteristics are very close to 3 dominant : 1 recessive, keep that in mind."Pea Green" is a color most people are familiar with, but this is the recessive color. The dominant trait of peas is yellow seeds; this is a great example of the dominant allele not necessarily being the common allele.

evidence of evolution

1. Direct observation 2. Homology -Anatomical, Embryological, and Molecular 3. Fossil evidence 4. Biogeographical evidenceScientists continue to collect data that supports the Theory of Evolution by Natural Selection.These are the four primary areas of research that are used to support the Theory.

Triple X Syndrome

47, XXX occur about 1 in 1,000 live births and have few, or no symptoms. These women are fertile in adulthood and may never be diagnosed. Women with Triple X syndrome carry 2 Barr bodies in each cell.

jacobs syndrome

47, XYY occurs about 1 in 1,000 live births and have few, or no symptoms. The most common symptoms are learning disabilities and excessive acne due to high, but normal, levels of testosterone. It was once believed that XYY males were more violent due to high levels of testosterone. This was disproven by a study of the prevalence of XYY in populations of men in prison and men that have never been to prison. There was no statistically significant difference in the occurrence of XYY between the populations. XYY nondisjunction can only happen during sperm formation.

DNA Microarray Assay

A tool to evaluate activity of many genes quickly• Each "spot" represents a different gene• Fluorescence indicates gene activity. A DNA Microarray assay is a way of analyzing the expression of hundreds of genes simultaneously. A microarray "chip" contains hundreds of attached, known gene fragments. The chip is washed with cDNA derived from different tissues or from cells in different stages of development; this is the probe DNA. The probe DNA is tagged with a fluorescent molecule that glows when the probe DNA binds with DNA on the chip. From the image above the probe DNA came from two different tissues within the same organism. Spots that glow red indicate that the gene at that spot is functional in tissue 1. Spots that glow green indicate the gene at that location is functional in tissue 2. Yellow glowing gene spots indicate the gene is functional in both tissues while black/gray spots indicate that the gene is not active in the tissue. A map of the genes on the chip is known to the researcher.

recessive allele

An allele that is masked when a dominant allele is present

Blood Types

An individual with Type-O does not carry type A or type B carbohydrates in the body, and therefore produces Anti-A and Anti-B antibodies. Type-O individuals can accept Type-O blood through transfusion, but if Type-A, Type-B, or Type-AB blood is transfused into a Type-O individual agglutination (clotting) will occur as an immune response. The only way agglutination by incorrect blood type is survivable is if it occurs in a hospital setting where the patient is treated with anti-coagulants drugs while flooding the veins the correct blood type.Individuals with Type-A blood carry only Anti-B antibodies as their body expects there to be Type-A carbohydrates present. A person with Type-A blood can receive Type-A blood or Type-O blood, because Type-O carries no carbohydrates. Type-A blood cannot receive Type-AB blood because, while there is the A carbohydrate, there is also the B carbohydrate.Individuals with Type-B blood carry only Anti-A antibodies as their body expects there to be Type-B carbohydrates present. A person with Type-B blood can receive Type-B blood or Type-O blood. Type-B blood cannot receive Type-AB blood because, while there is the B carbohydrate, there is also the A carbohydrate.Individuals with Type-AB blood do not react to the presence of A or B carbohydrates since they would naturally be present. Type-AB individuals can receive any blood type (not including Rh factor).Type-O blood is the "universal donor" because Type-O, Type-A, Type-B, and Type-AB can receive this blood without causing an immune response. If an individual has Rh-positive blood, they can receive Rh-positive or Rh-negative blood. Individuals with Rh-negative blood type can only receive Rh-negative blood because they produce Anti-Rh antibodies.Individuals with AB-positive blood type can receive any type of blood with no reaction.O-negative blood can give blood to anyone (but can only receive O-negative). In an emergency individuals are given O-negative blood because it won't cause a reaction regardless of the injured person's blood type.

Analogous/convergent evolution

Analogous structures are those that are similar due to use, not shared ancestry and arise from convergent evolution.

CRISPR/Cas 9 gene editing

CRISPR-Cas9 takes advantage of bacterial immune system function to target and alter genes. CRISPR-Cas9 is the latest, and perhaps most promising, method of gene editing. It is derived from the immune system used by bacteria. The bacterial Cas protein holds an RNA sequence that is used to target and cut a DNA fragment. In the natural system bacteria destroy invading viruses by retaining a portion of a virus from a previous infection. The retained portion is used as the targeting sequence to target a new invading virus. Interestingly, this system is hereditary in bacteria with "parent" bacteria transmitting up to 30 different sequences to "offspring". Current research has been successful in using CRISPR-Cas9 to cut "bad" DNA sequences but has been hampered in the effort to insert the "good" DNA sequence that would cure and individual of a genetic disorder. When this technology becomes efficient, cured individuals will still pass the incorrect ("bad") copy of the gene to their offspring, unless the CRISPR Cas 9 system is activated on gamete producing cells. That technology is a very long way off and crosses a line in the world of bioethics.

epigenetics and cloning

Cloned individuals do not look exactly alike and do not behave alike• A cloned animal expresses genes differently due to acetylation and methylation. While a cloned individual and its clone share the same DNA, they may not look exactly alike. These female calico cats have slightly different coat patterns despite one being a clone of the other. The differences are due to inactivation of X-chromosomes in different cells during development.

Biotech: DNA fingerprinting

Colin Pitchfork was the first perpetrator of a crime convicted using DNA evidence. In 1983 and 1986 two young teenage girls were each found raped and strangled in Leicestershire, England. Blood type analysis revealed that a man with Type-A blood had committed both crimes and based on the nature of the attacks it was believed it was the same man that committed both crimes. As DNA technology became available the local police department set out to collect DNA from all the local males to find a match to the semen left on the victims. After the initial screening, no suspect was identified as a match to the semen. The semen was confirmed to have come from the same man though. In 1987 Ian Kelly, a coworker of Pitchfork's, was overheard in a bar discussing giving a DNA sample under Pitchfork's name. Upon police questioning, Kelly stated that Pitchfork said he had given his own DNA for another individual and therefore couldn't provide his own sample because he would be caught for giving the fraudulent sample. Pitchfork was compelled by the court to give a sample, which was a confirmed match to the semen left on the two young girls. Pitchfork was sentenced to life in prison, his sentence was reduced to 28 years, and he has since been moved to an "open prison" where he is released, unsupervised during the day.

comparative embryology

Comparative embryology allows for comparison in early developmental genesComparing embryological development allows for a comparison of the expression of the most basic genes. These are genes that determine the formation/shape of a body and the formation of all organs. It is assumed that these genes that define a body are the most primitive genes.From the image above, both chicken and human embryos carry pharyngeal arches (primitive gills) and a post-anal tail (a tail that extends beyond the anus), but neither of those structures are present at birth. It is hypothesized that these ancient genes are turned on during early body formation, but then "newer" genes turned on later in embryo development "undo" those primitive characteristics. Occasionally, a human is born with a reduced tail that results from failure of genes turned on later in development and are responsible for the reduction of the tail to the fused tailbone (coccyx). Individuals born with a tail typically have surgical correction shortly after birth.

RNA genome sequencing.

Comparing sequences by tissue indicates which genes are expressed and at what level. The DNA sequence of a protein-coding gene can be determined by RT-PCR and reassembly of the cDNA sequences. mRNA, representing active genes, is extracted from a cell and cut into small fragments. The fragmented mRNA is then reverse transcribed, providing DNA fragments small enough for sequencing. The sequence of the fragments is re-assembled into a gene sequence using computer programs to align overlapping portions of the fragments. It is like trying to put together a puzzle without a picture.

Anatomical Evidence

Comparison of the bones of the upper limb reveal homology across wide-ranging species• Comparison of bone structure is especially important in fossil studiesLooking at the forelimb of a variety of organisms reveals the homologous nature of the bone structures. The upper arm contains a single strong bone called the humerus (colored pink). The Humerus provides strength for muscle attachment and support.The lower forelimb contains two bones, the radius and the ulna (yellow = radius, blue = ulna). The presence of two bones allow for rotation between the upper and lower arm. Within the wrist are numerous bones that allow for near-360orotation. The uncolored bones are the metacarpals (hand bones) and phalanges (finger bones). The fact that the same bones exist in the forelimbs of most vertebrates gives two possibilities.1. Each species evolved this body plan because there was an advantage to the plan (that is, this set of bones evolved thousands of times).2. An ancient ancestor possessed this bone structure and did well because it was an advantage. That species survived and diversified over millions of years (dinosaurs have the same bone pattern) so that we see the same order of bones in thousands of species today.Occam's razor states that the simplest answer is usually the correct answer. In this case, the simplest explanation is that this body plan is a shared characteristic; shared with an ancestor that predates the age of the dinosaur.

convergent evolution

Convergent evolution occurs when unrelated species living in similar environments take on a similar appearanceConvergent Evolution occurs when similar anatomy is seen in very different species that live in similar environments. For example, the Australian Sugar Glider is a marsupial tree-dweller with large skin flaps that allow it to glide from tree to tree. Similarly, the flying squirrel is a North American mammal with large skin flaps that allow it to glide from tree to tree. These two species, living in distant but similar environments, each evolved the skin flap separately and is not the result of shared ancestry. There are many examples of animals with shared body type based on their function/role in similar environments

artificial selection as a model

Cruciferous vegetables are all descendants of the wild mustard• Regional preference led to today's varietyIt is difficult to witness Natural Selection because it takes many generations to see significant change; that is difficult to witness within a single human lifetime.Artificial Selection can be used to model Natural Selection.Artificial Selection is completely human-driven. In nature, individuals who aren't best suited may still reproduce but at a lower rate. In Artificial Selection only the highest performing individuals (for what ever the trait is) can breed; all others are destroyed. Artificial Selection explains how there is so much variety in the Cruciferous vegetables developed in the past 10,000 years. All these plants originated from a wild mustard species; as humans traveled and exchanged goods with other groups of humans the seeds of the edible wild mustard were spread world-wide. Individuals in different areas of the world planted and selected individuals for different traits that led to today's varieties. Imagine the time and energy spent to maintain a garden, would you collect and re-plant seeds from a plant that doesn't taste as good as another plant? No, you wouldn't. Seeds are gathered from the best tasting plants and from the plants that produce the most food and only those seeds are planted the next growing season.

DNA profiling

DNA profiling matches suspects with evidence • DNA evidence is used to convict perpetrators as well as exonerate those that have been wrongfully convicted. DNA profiling relies on Short Tandem Repeat (STR) markers determined by PCR analyses. Each of us carries a large quantity of non-coding DNA, where mutations have little to no effect on an individual. Within these non-coding regions, we carry some repeated DNA sequences of differing lengths, due to different numbers of repeated units. In 1984 Earl Washington was convicted of the 1982 rape and murder of 19-year-old Rebecca Lyn Williams. DNA technology was later applied to evidence from the case as part of the Innocence Project. DNA analyses use differences in these non-coding regions to identify individuals. Earl Washington carries two different STR repeat numbers for each of three STR markers used. For STR marker 1 he carries 16 repeats on one chromosome and 18 on the other. For STR marker 2 Earl Washington carries 14 repeats on one chromosome and 15 on the other, while he carries 11 and 12 repeats for STR marker 3.An analysis of the semen from the rape shows that the semen donor, and perpetrator of the murder, carried marker repeats at all three STR locations that are different from Earl Washington's. This data was used to exonerating Earl Washington after 17 years in prison. Analyses of Kenneth Tinsley, a sexual predator convicted of rape in 1984, shows that he is the correct match to the semen, and it is statistically certain that he was the perpetrator of the rape. In 2007 Kenneth Tinsley confessed to the rape and murder and additional time was added to the sentence he was already serving for rape. Earl Washington was released from prison in 2000 and settled a lawsuit with the state of Virginia. He is currently married and living in Virginia.

DNA sequencing gel

DNA sequencing gels are read in sets of four columns• Repeating patterns within the DNA can be selected and identified. This is a DNA sequencing gel from a species of rare plant, Lobelia boykinii. I produced this gel about 20 years ago while investigating repeated DNA sequences within the genome of the species.I have highlighted four of those repeated sequences. Each vertical column represents a nucleotide (A, C, G, or T); in the highlighted boxes repeated sequences are visible. The first box shows a repeat of A-C, note that the next two columns to the right of the box are empty in the corresponding region, that's because there are no G or T nucleotides in that stretch of DNA.To create this image, DNA was extracted from individual plants, dideoxynucleotide PCR reactions were run, and the PCR products were separated on this gel. The gel is 0.2mm thick polyacrylamide gel that allows high resolution of DNA fragments. It took 6 hours to simply run this gel and several more hours to analyze the data. I was the first person to ever sequence and visualize DNA from this species.

Darwin's observations

Darwin primarily focused on gathering information regarding fossils and local adaptations. Darwin's primary observations were of fossils and adaptations in living organisms.In South America, Darwin found fossils of the extinct Glyptodon and suggested that it was perhaps related to the modern-day Armadillo. For perspective Glyptodons weighed over 4,000 pounds, while modern Armadillos weigh under 15 pounds.

darwins proposition

Darwin proposed that organisms descended from common ancestors• Over time there were changes in each lineDarwin's famous "I Think" sketch as he worked out the concept of descent with modification (Evolution).

Galapagos Finches

Darwin was amazed with the diversity of finches on the Galápagos Islands• These birds helped form Darwin's theory of Natural Selection as the driving force for Evolution.Darwin was amazed by the diversity of finches he found on the Galápagos Islands. He found 15 different species of finches with a wide diversity in beak and body shapes; far more diversity than in finch populations in South America.Darwin predicted that a few birds arrived on the Islands following storms, and then spread across the islands adapting to the available food sources.

Voyage of HMS Beagle

Darwin's journey around the world revolutionized his perception of natural history.Darwin was brought on board the HMS Beagle to serve as a Naturalist that could identify important resources for the British Royal Navy. Due to social constraints, the Captain of a ship would not "mingle" with the crew; Darwin was an equal in intellect and served as a travelling companion for the Captain of the HMS Beagle.Charles Darwin experienced sea sickness and found the reading helped alleviate the feeling. During his travels Darwin read Lyell's Principles of Geology multiple times. As he started exploring the Andes Mountains and found fossilized seashells in the mountains, he began to apply the processes of gradualism and uniformitarianism to what he witnessed. Once in the Galápagos Islands, Darwin was awestruck by the diversity of life and began to fully hypothesize on the origin of those life forms.

artificial selection

Diversity of modern dogs arose from regional preference as dogs were domesticated from wolvesArtificial Selection led to the modern Dog. Genetic evidence suggests dogs evolved from wolves about 15,000 years ago when humans were still hunter-gatherers. The hypothesis is that as humans gathered and ate, we would leave food scraps that some wolves would come and feed from. Those wolves, but not all wolves, started to associate humans with food. The ancient dog helped protect human populations from other predators because it meant protecting their own food source. The relationship became closer when humans began intentionally feeding the new dogs who then slept with their humans, providing heat and protection. Those wolf individuals that were uncomfortable with the close arrangement remained wild wolves.After domestication human groups traded puppies, and as the domestic dog spread globally different traits were selected as desirable. Some dogs were selected to assist with hunting, others with herding, and then there is the Chihuahua. The Chihuahua was developed in the Mexican state of Chihuahua and became essential in the fight against rats in primitive sewer systems. The dogs are small enough to fit through pipes, and vicious enough to kill a rat half it's size.

genetic linkage experimentation

Evaluating the number of recombinant offspring resulting from a mating allows for a calculation of the distance between genes. In Drosophila the genes that control body color (b+ = gray, b = black) and wing length (vg+ = normal, vg = vestigial/reduced) are located near each other on chromosome II. Note that a slightly different genetic notation is used here. The "+" sign indicates the dominant wild-type condition.An experimental cross is completed to estimate the distance between the linked body color and wing length genes. The female displays the dominant phenotypes, gray body and normal wings, but is heterozygous for these two traits (b+b, vg+vg). Due to their proximity these two traits previous experimentation showed that they do not follow Mendel's Law of Segregation as expected. Because the genes are commonly inherited together the female carries one chromosome with two dominant alleles while the homologous chromosome carries two recessive alleles. During Prophase I of Meiosis genetic recombination (crossing over) may occur between the two homologous chromosomes resulting in two recombinant chromosomes, each with one dominant and one recessive allele. The female will produce eggs that contain either a "Parental" chromosome or a "Recombinant" chromosome. The male used in this cross is homozygous and can only produce one combination of genes (black body paired with vestigial wings). After mating the heterozygous female with the homozygous recessive male their offspring will be collected and scored for body color and wing length. "Parental type" offspring look like one of the two parents: gray body with normal wings OR black body with vestigial wings. "Recombinant" offspring do not look like either parents and have a new combination of traits: gray body with vestigial wings OR black body with normal wings.By looking at the proportion of offspring that carry the new combination of characteristics the recombination frequency can be calculated. The recombination frequency is used as a measure of the physical distance between the genes.Parental gray body with normal wing count: 415Parental black body with vestigial wing count: 405Recombinant gray body with vestigial wing count: 92Recombinant black body with normal wing count: 88The recombination frequency is calculated as: (number of recombinant offspring/total offspring) x 100. In this case: 180/1,000 x 100 = 18%

xdrTB

Extreme drug resistant Tuberculosis (xdrTB) is a serious global threatTuberculosis is a bacterial infection of the lower lungs. The bacteria form thick-walled nodules called tubercules that protect the bacteria from antibiotics. Tuberculosis is an air-borne disease spread by coughing. There are some antibiotics that are effective against Tuberculosis, but as antibiotic use increased so did the bacteria's resistance to those antibiotics.There are now drug resistant strains of Tuberculosis, including extreme-drug-resistant (xdr) Tuberculosis strains, that are resistant to all known antibiotics.

F1 x F1 cross

F2 generation. the f2 phenotypic ratio is 3:1.The same procedure is used to match Parent 1 gametes with Parent 2 gametes to form the F2 offspring in the squares of the Punnett square. Recall that the genotype and phenotype are both included in the resulting F2 offspring squares.Having found the F1 ratio (1:0) and the F2 ratio (3:1) the problem is complete.The 3:1 ratio should look a little familiar to you. This is the ratio Gregor Mendel arrived at for each of the 7 different pea characteristics.

gametes for a two-trait cross

For an individual with the genotype TTRR the gametes would be:TR and TR and TR and TR• Determine the gametes for an individual with the genotype ttrr. To determine the gametes used in a two-trait cross the genotype cannot simply be divided in half as was done with a one trait cross. If that method was used it would produce gametes with two copies of one gene and no copies of the other and be in violation of Mendel's Law of Segregation.There is a tool that can be applied for determining gametes in a two-trait cross. That tool is called FOIL, the same FOIL from algebra class. Using FOIL one can determine every possible allele combination an individual can produces in their gametes.When an individual is homozygous for both traits, they can only produce one kind of gamete and the FOIL method gives that gamete four times.

genetic linkage

Genes follow Mendel's laws of Independent Assortment and Segregation when:-On different chromosomes-On the same chromosome but are very distant• Genes near each other on the same chromosome may be linked genes. Genetic linkage occurs when genes reside near each other on a chromosome. The probability of a chiasmata forming between two physically close genes is very small, so the genes are usually inherited as a group.Mendel was "lucky" in that the seven characteristics he studied were on seven different chromosomes (there are only 7 in peas) and therefore showed no linkage of traits. It is rumored that Mendel looked at other traits but was frustrated by being unable to understand how they were inherited. It is also rumored that some of Mendel's assistants would intentionally remove plants displayed character combinations they knew would upset Mendel if he saw them. He was only human.

linked genes

Genes near one another on a chromosome are typically inherited together• Formation of a chiasma between these two genes is rare and the only mechanism to "separate" the linked allelesGenes that are near each other can only be separated if a chiasmata forms between those two genes during Prophase I of Meiosis. The odds that a chiasmata forms in that exact location is quite small and the odds that that gamete participates in fertilization further reduces the odds of seeing these genes separated.Research indicates that genes related to alcoholism, psychiatric disorders, diabetes, and cardiovascular disease may be linked. While each of these conditions is likely polygenic, and are impacted by the effect of the environment, it is wise to be cautious if you know of a family history of one of these conditions your risk of experiencing these conditions increases.

GMO- food

Genetically Modified Organisms have been a part of the food stream for decades• The use of GMO food supports the growing human population.Genetically Modified Food -a subject of hot debate. Is it safe? Should we eat it? Will it change us if we do?There are many foods that have been genetically modified, many to allow for faster growth and tolerance to herbicides. Golden rice, above, was modified by including a gene from daffodils so that the rice produces beta carotene, the precursor to vitamin A. It is estimated that Vitamin A deficiency-blindness could be eliminated with the cultivation of Golden rice. Every year about 250,000 children go blind due to vitamin A deficiency. There has been resistance from governments about the safety of Golden rice and it has not been grown for human consumption in any country yet.The truth is, with a growing human population, expected to reach 12 billion by the end of the century, we will need to grow more food per area of land to feed all the people on earth. GMOs are one of the few ways we can increase crop productions to support the human population. We live in a country with ample food supplies and therefore have the luxury and privilege to reject GMO foods.

Natural Selection details

Heritable Variations• More offspring than can be supported• Differential Reproductive Success• Favorable trait becomes more prevalent.Darwin's Theory of Evolution by Natural Selection hinges upon the processes of Natural Selection. It is the description of Natural Selection that Darwin explained that was ground-breaking. Scientists had some agreement that species might change, but there was no explanation for HOW they changed.Natural Selection occurs through several steps: 1. It relies on heritable variation; that is variations that are carried in genes. This differs from Lamarck's hypothesis that was the inheritance of traits an individual accumulated during their lifetime. 2. More offspring must be born into an environment than can be supported. This sets up competition for resources such as food, light, water, nesting sites, etc. 3. Those individuals that carry the inherited traits that allow them to out compete others will have greater reproductive success. Those individuals that are more successful at finding food have greater ability to find a mate and reproduce. Individuals that can out compete another for a nesting site will get to reproduce and pass their genes on. Individuals that don't succeed in competition don't get to reproduce (or reproduce very little) and eventually those genes are lost from the population. 4. As the more successful individuals breed each generation the proportion of advantageous genes increases. That is, the characteristic that helped an individual gain more food, or find a nesting site will become common. When most individuals carry the "good" trait a new trait will be selected and promoted in the population (building on Malthus' hypothesis on populations).

incomplete dominance

Heterozygous phenotype is an intermediate of the two homozygous phenotypes. With Incomplete Dominance the dominant allele cannot completely mask the presence of the recessive allele. In this case a heterozygous individual will express a phenotype that is an intermediate of the two parental phenotypes. While the Punnett squares for these types of crosses are set up the same way, the Phenotypic Ratio is given as:Number of homozygous dominant offspring : Number of heterozygous offspring : Number of homozygous recessive offspring In the image above a white-flowered plant is mated with a red-flowered plant to produce pink-flowered plants in the F1 generation. If pink-flowered plants mate, or self-pollinate, they produce offspring in a 1:2:1 ratio of red : pink : white.When it is unclear which gene is dominant notation is used to indicate that alleles are variations of a gene. That notation is shown in the figure above where R = red pigment and R' ("R-prime") = white pigment.

example of relationship of phenotype and genotype

Hold up your hand in a natural position. If your ring finger is the same length, or shorter than your "pointer finger" then you have the phenotype "Short Finger". If your ring finger is longer than your pointer finger then you have the phenotype "Long Finger". If you, like most humans, have the short finger phenotype you are either homozygous dominant (that is, you have two copies of the "short" allele) or are heterozygous (one copy of "short" that masks one copy of "long"). Remember, you have two copies of each chromosome/each trait, therefore you have two letters to represent those two alleles. If you have the short finger phenotype you don't know your genotype (it's DD or Dd, but you can't tell), if you have the long finger phenotype then you do know your genotype, it is dd, the only genotype that can give the phenotype long finger.

when is an individual considered heterozygous

If an individual carries two different alleles they are Heterozygous for that trait.

setting up a two-trait cross

In a two-trait cross two different traits are evaluated at the same time• Two trait crosses follow the same principles and rules of a one-trait cross• The genotype must include both alleles for both traits, so each individual will have a genotype that contains 4 letters. ex. Let's extend our plant height cross and include seed shape. Round seeds (RR or Rr) are dominant while wrinkled seeds (rr) are recessive.Problem: A true-breeding tall plant that produces round seeds is mated with a short plant that produces wrinkled seeds. Find the F1 and F2 phenotypic ratios. P-Generation: Parent 1, Parent 2 Phenotype: Tall-Round Short-Wrinkled Genotype: TTRR ttrr Gametes: Hmmm ... that seems a little tricky

mendels laws

In reviewing the Law of Independent Assortment, we see that every possible combination of alleles can be formed. In this case one parent carries two dominant seed color alleles (YY) on homologous chromosomes and two dominant seed shape alleles (RR) on another set of homologous chromosomes. The second parent carries two recessive seed color alleles (yy) on homologous chromosomes and two recessive seed shape alleles (rr) on another set of homologous chromosomes.The individuals of the F1 generation carry one dominant and one recessive allele for each of the two traits. The F1 individuals have the alleles YyRr. As the F1 individuals complete Meiosis to form gametes the Law of Segregation and the Law of Independent Assortment both come into play in the formation of those F1 gametes. The Law of Segregation says that the maternal and blue paternal chromosomes carried in the F1 individual separate from each other during gamete formation.Combining these two laws means that an individual's gametes will carry only one of each chromosome and chromosomes are now paired with the same or opposite parental non-homologous chromosomes. Gametes that carry the original Parental combination (YR or yr) are considered Parental gametes, while the gametes that carry a new combination (Yr and yR) are termed recombinant gametes.

variations on mendel's laws

Incomplete Dominance• Codominance• Multiple Alleles• Pleiotropy• Epistasis• Polygenic Inheritance (and Environment). In the end Gregor Mendel answered his question "How do parents provide information to children" and was pleased with himself. Just imagine, he did all of this with NO knowledge of DNA! Mendel did publish his ideas in 1865, but they were generally not understood for their true importance. Mendel died in 1884 and much of his work was lost in a fire at the monastery where he lived and studied. It wasn't until the early 1900s that his work was rediscovered and understood for its importance. One of the major criticisms of Charles Darwin's Theory of Evolution presented in 1859, was the lack of understanding of inheritance. It is believed that had Charles Darwin read, and understood Mendel's work the Theory of Evolution by Natural Selection would have received greater acceptance at the time. There were events that Mendel witnessed and could not explain, so he ignored them -he was human after all. Since Mendel's time those events have been studied and come to be understood.

which blood type is the most common globally?

It's type-O at about 54% of the world population! Type-AB is the rarest. This is an example of a phenomenon called Genetic Drift, where just by chance certain alleles become common or rare.

MRSA- USA300

MRSA acquired several key mutations that make it a persistent and fatal organismMethicillin Resistant Staphylococcus aureus (MRSA) is an adapted bacterial strain that is capable of invading through the skin and entering the bloodstream, possibly leading to death. As well, it has picked up resistance to methicillin-type antibiotics which makes it difficult to treat MRSA infections. Did MRSA exist before antibiotics? Yes and no. Staphylococcus aureus is a common bacterial strain that up to 70% of healthy adults carry in their sinus cavities. S. aureus, like every other species on Earth carries natural genetic variation within its populations. Methicillin-resistant strains of S. aureus are a new variety of the bacteria that developed only after antibiotics came into common use, as there was no selective pressure to antibiotics before then. As individuals began taking antibiotics most of the bacteria were killed, but those bacterial individuals with the genetic predisposition to survive the antibiotic were unharmed and could then reproduce and repopulate.When did we start taking antibiotics? After World War II, starting in the mid-1940s, about 75 years ago.

male- pattern baldness

Male-Pattern baldness begins in a variety of manners• Some women also experience male-pattern baldness, typically following pattern 2 or 4.Red-green colorblindness and male-pattern baldness are two common, non-fatal X-linked human characteristics.Male-pattern baldness occurs in several patterns, but regardless of the pattern the result is the same. While it is less common, women also experience male-pattern baldness. Women typically experience thinning hair on the top of the hair; the thinning patch expands over time.You may be wondering/worried about whether you will experience baldness. The best predictor of whether anyone will go bald will be to look at the hair condition of your mother's father (maternal grandfather). If your maternal grandfather is bald then your mom is heterozygous for the baldness trait (XBXb); her sons have a 50% of going bald. It is possible for a man to go bald even if his maternal grandfather has a full head of hair, but the likelihood decreases dramatically. Since fathers pass their Y-chromosome to their sons it doesn't matter if a man's father is bald. For a woman to go bald her father must be bald (XbY), and her mother must be either heterozygous (XBXb) or balding herself (XbXb). Individuals of European descent are more likely to go bald, but it is a trait found in all human populations.

Pleitropy

Marfan Syndrome. occurs when one genotype results in multiple phenotypes. Pleiotropy is a situation where a single gene gives multiple phenotypes. Marfan Syndrome is caused by a single gene defect that affects connective tissue. The way in which that connective tissue defect presents itself in a patient is different in everyone. A doctor visits with 3 patients each with different medical issues such as: scoliosis and joint problems, a dislocated lens in the eye, and a hernia. While the three patients present different conditions, the conditions are all caused by the same genetic defect.

Principle of Segregation

Mendel formed two theories of inheritance, the first was the Law of Independent Assortment discussed in the Meiosis chapter. The Law of Independent Assortment is one of the contributing factors in genetic diversity of gametes.The second theory Mendel proposed was the Principle of Segregation (also called the Law of Segregation). Note, the word Segregation means to separate, and that is how the word is interpreted here.Mendel knew nothing of alleles, in fact, DNA wasn't even established as the genetic material until more than 40 years after his death. Mendel called the inherited material that was passed from parent to offspring "factors", today we understand "factors" to be alleles. 1. The two factors/alleles each individual carries came from their parents, one from each. 2. During gamete formation within an individual the two factors they received from their parents will separate from each other (separation of homologous chromosomes). 3. Each gamete contains only one copy of each chromosome (that chromosome carries one factor/allele for each trait). 4. The combination of gametes in fertilization restores two factors/alleles to the new individual.

corn development

Modern corn was developed in Mexico's Tehuacán valley from a grass species called TeosinteThe Tehuacán Valley of Mexico is thought to be a major center of plant domestication that began about 8,000 years ago. Corn is derived from Teosinte ("tee-o-sin-tay"); a grass species still present today. Teosinte forms small cob-like structures that carry multiple seeds encased in a rigid seed coat. Teosinte plants have multiple branching stems that each support these small cobs of seeds. In the aggressive selective breeding of modern-day corn, the lateral branches were reduced while the cob size was increased dramatically. As well, the rigid seed coat has been lost, making the seeds more palatable and useful in a variety of manners.

experimentation

Modern day experimentation continues to provide support for the theory of Evolution by Natural SelectionScientists studying Evolution look at fossils, biogeography, molecular and anatomical homology, and embryology. Many scientists, like Dr. Lenski, conduct on-going experiments. Guppies are small, live-bearing fish frequently found in home aquariums because of their easy maintenance and bright colors. In the wild, guppies display different color patterns depending on the size of the pond they live in, and the types of other fish present. Male guppies with brighter coloration attract more females, like the flashy style of peacocks. In ponds that contain pike-cichlids the adult guppies have less bright coloration and fewer color spots, thus allowing them to avoid predation by the pike-cichlid. In ponds that lack pike-cichlids, but contain killifish, the adults have brighter color and more color spots because killifish only prey upon colorless juvenile guppies. In the killifish ponds there is an advantage to being colorful, mate selection, and no apparent disadvantage. Transplanting "drab" guppies from pike-cichlid ponds to killifish ponds results in an increase in offspring with bright coloration. In the pike-cichlid ponds the brightly-colored adult males are eaten by pike-cichlids, so bright coloration is a less favorable characteristic. In the killifish ponds brightly-colored males are preferred by females and there is no drawback to being brightly colored; over time the population of guppies in the killifish ponds became more brightly colored and carried more color spots. When a population changes Evolution occurred. The population of transplanted drab guppies carried the heritable trait for bright coloration and numerous colored spots. In the new environment the guppies experienced a population explosion which allowed for selection of favorable traits, in this case the female preference for brightly-colored males. As more brightly-colored males produced more offspring than their drab counterparts the brightly colored trait became more common. Within a short period of time the entire guppy population, derived from the original drab transplanted guppies, became brightly-colored.Bio 151 - Chapter 21

Molecular evidence for evolution

Molecular evidence represents changes in DNA over time• Timelines are estimated using mutation ratesScientists use molecular data to make comparisons between species as well. There is an added benefit of a "molecular timeline" that can be estimated from molecular data. When the mutation rate and the number of nucleotide differences between two species are known, it is a simple mathematical calculation to determine how long ago the two species shared a common ancestor.Molecular comparisons can be performed directly by DNA sequence comparisons, or indirectly through comparisons of amino acid sequences of proteins.Above is a comparison of the Cytochrome c mitochondrial membrane protein sequence in a variety of organisms. If you recall, Cytochrome c is a protein essential in the transfer of electrons in the Electron Transport Chain of Cellular Respiration. Cytochrome c contains 100-104 amino acids, depending on species. There is extreme pressure on maintaining the "correct" version of the protein, thus all humans carry the exact same amino acid sequence of Cytochrome c protein. Monkey sequences that have been evaluated have one amino acid difference from humans. The greatest known amount of change (50 amino acids difference) in eukaryotic species is between human and yeast (the organism used to make beer, wine, and bread). We share 50% of the Cytochrome c genetic information with a yeast cell.*Let's address a common fallacy in the anti-Evolution stance. The fallacy is this: If humans came from monkeys, then why are there still monkeys.Humans didn't come from monkeys ("IF humans came from monkeys...")Humans and monkeys share a common ancestor. That last common ancestor was a primate from which all modern-day primates originated. The last common ancestor of primates didn't look like a monkey, or a human, it was its own species. The last common ancestor of Humans and Chimpanzees (our closest relative) lived about 8 million years ago. The last common ancestor of all primates is estimated to have lived about 25 million years ago.

Cit + E.Coli

Mutation appears around generation 33,000• Going back to frozen vials initial mutation occurred around generation 20,000How did Lenski's bacteria start to metabolize citrate?Going back to the frozen samples, analyses show that mutations began to accumulate in population #3 around the 20,000th generation. The research group began re-growing cells from the frozen populations to try and determine at what point enough mutations were acquired to lead to citrate digestion. All cells re-grown from generation 31,500 led to cells with the Cit+ genotype/phenotype. This indicates that mutations beginning at generation 20,0000 led to a cascade of mutations that culminated in the bacteria's ability to use citrate as a food source.As of March 9, 2020, the Lenski lab is closed, and all populations placed in ultra-low temperature storage due to COVID-19 closures.On May 4, 2020, Dr. Lenski received a grant renewal to continue the research. It was also announced that the research project would be transferred to Dr. Jeffrey Barrick at the University of Texas -Austin.

Next- Generation DNA sequencing

Next-Gen Sequencing is more rapid and accurate• Computer readouts are interpreted to reveal sequence. Sanger Sequencing, while great at the time, was a time-consuming process. Next Generation Sequencing allows for rapid results using flashes of light produced when phosphate groups are released. The flashes of light are recorded by a light-detecting sensor. The results are provided in a bar graph that indicates the number of each nucleotide in a row. A single nucleotide produces a level 1 flash, while 2 or more of the same nucleotide in a row will produce increasing flash intensities, indicating the number of nucleotides. The sequence is then read and assembled by computer programs.Partial DNA sequences (not the whole genome) are sequenced in a matter of hours.

how to cross peas

Pea plants normally self-pollinate. In fact, pea pollen is released before the flower opens, thus ensuring near 100% self-pollination. Peas are relatively easy to work with in forcing specific cross-pollination matings. A pea flower can be opened with a dissecting needle before pollen has been released and one can remove the stamen native to that flower (stamen produce pollen, the "male part" of a flower). While the flower is open ripe pollen from another flower is retrieved and brushed onto the stigma (the "female part" of a flower) of the flower that had its stamen removed. The flower is closed back up and allowed to develop normally. easily cross-polinated by hand.

when were punnett squares developed

Punnett Squares were developed by Reginald Punnett (1875-1967) as a way of estimating the outcomes of a mating. There is a Khan Academy video out there that says Punnett squares got their name from produce baskets... not true!

Qualifying DNA by Fluorescence

RT-qPCR is used to quantify the amount of DNA in a sample while the PCR process is running.

two-trait cross details

Recall that the size of the Punnett Square is determined by the number of different gamete possibilities.Having applied FOIL to each parent, the gametes that parent can produce have been determined and the problem can be set up completely:P-Generation: Parent 1 Parent 2Phenotype: Tall-Round Short-WrinkledGenotype: TTRR ttrrGametes: TR trFollow the same procedure as in the one-trait crosses. Gametes from parent 1 and parent 2 are matched to fill a square. Always combine the two alleles for the same gene together; doing so makes it easier to determine the phenotype of the offspring. While you *could* write TRtr in the first square, students tend to make errors in determining the phenotype when the alleles are arranged this way. If the phenotypes are incorrect then the phenotypic ratio will be incorrect. Only one type of offspring is possible in this cross, heterozygous tall plants with round seeds (TtRr).

red-green color blindness

Red-green colorblindness affects 1 in 12 (8%) men and 1 in 200 (0.5%) women. World-wide there are about 300 million people with red-green colorblindness. It is not uncommon for individuals to move through life without knowing they are red-green colorblind. Red-green colorblindness is caused by a gene carried on the X-chromosome that is responsible for producing color-receiving cones embedded in the retina of the eye. Individuals with red-green deficiency cannot distinguish between certain wavelengths of light and experience color confusion between blue/purple, green/yellow, pink/white most commonly.Color deficiency vision is diagnosed by an eye health professional using Ishihara's color plate images, like the one above. The color plates are made with special inks reflect specific wavelengths of light. If you have trouble reading the number "3" in the image above do not worry, this is a graphical representation of an Ishihara's color plate and cannot be used for diagnosis.Like male-pattern baldness affected males carry one X-chromosome with the recessive gene; this defective X-chromosome is inherited from a man's mother. Males have the genotype/phenotype combinations: XGY/normal vision or XgY/color deficient.Females have the genotype/phenotype combinations: XGXG/normal vision, non-carrier; XGXg/normal vision, carrier; or XgXg/color deficient.As I mentioned in the previous chapter, my oldest son is red-green color blind which means I am a heterozygous carrier. We recently got the color blindness "correcting" glasses for him and he has seen dramatic results. The glasses work by dividing wavelengths of light into smaller segments allowing individuals to more easily discern differences between wavelengths. This fall was amazing for him as the changing leaves only ever looked yellow to him before.

cloning technology

Reproductive cloning produces an entire organism -like Dolly the Sheep. Cloning technology is used in two different ways: Reproductive Cloning and Therapeutic Cloning. Both varieties of cloning are based a process called nuclear transfer where a diploid nucleus is transplanted into an unfertilized egg cell that has had its haploid nucleus removed (enucleated).1. Reproductive cloning is used to make an entire organism from a somatic cell of the original organism. 2. Therapeutic cloning is used to make tissues and organs from a somatic cell of the original organism.Dolly the Sheep was the first successfully cloned mammal. Dolly had three "mothers", the mother that donated the nucleus, the mother that donated the egg, and the mother that acted as a surrogate to carry the pregnancy.While Dolly's life was shorter (6.5 years) than expected (10-12 years) she died of a type of lung cancer caused by a virus. Through studies of Dolly's cells, it was revealed that her telomeres were unexpectedly short.Reproductive cloning of humans is considered misconduct and is severely ostracized by the scientific community. Any researcher that attempts to report on human reproductive cloning will not be able to publish their works, and thus will not be validated.

soapberry bugs

Soapberry bugs' beak length shortened in a short time as a response to feeding on invasive goldenrain tree fruitSoapberry bugs have a "beak" that they use to penetrate fruit and suck up nutrients from the developing seeds. Soapberry bugs in southern Florida feed primarily on the native balloon vine fruit (upper right picture), while soapberry bugs in central Florida feed primarily on the introduced goldenrain tree fruits (lower right picture). Soapberry bugs that feed on the native fruit can only gain sustenance if their beak is long enough to reach the seeds in the center of the fruit, therefore, it is imperative to have a long beak (there is no "want" or "desire" here, it is do or die). Soapberry bugs that feed on the seeds of the goldenrain tree can gain nutrition with a shorter beak and have experienced a reduction in beak length over the past 75 years.

analogous species

Species that live in similar habitats and take on similar body types and functions are termed analogous speciesAll three of these birds share similar anatomy and behavior. Perhaps not surprising they also share similar habitats.All three are large, flightless, running birds that live in grasslands. They are analogous species because they do not share recent evolutionary heritage but do share body plans that originated from living in similar environments and experiencing similar evolutionary pressures.The birds are: (upper left) the Ostrich (Struthio camelus) native to the grasslands of Africa, (upper right) the Emu (Dromaius novaehollandiae) native to the grasslands of Australia, and (bottom) the Greater Rhea (Rhea americana) native to the grasslands of South America. These three birds are all members of the Class Aves and the subgroup Paleognathae

the y-chromosome

The X- and Y-Chromosomes carry small homologous regions (PAR1 and PAR2) that rarely cross-over• The Y-chromosome is usually passed father-to-son unchangedThe X- and Y-chromosomes align together as homologous chromosomes during Meiosis despite being non-homologous. Very rarely the X- and Y-chromosomes may exchange small regions at either PAR1 or PAR2 (never both at the same time), if a chiasmata forms during Prophase I. PAR1 contains 26 genes while PAR2 contains 5 genes. Since genetic recombination between the X- and Y-chromosomes occurs so infrequently the Y-chromosome passed from father to son is usually 100% identical.The Y-chromosome contains genes that are necessary for forming the male body and producing sperm.

Biogeography

The distribution of organisms by environments• The presence of fossils on different (present) continents supports the theory of Pangea and Continental DriftBiogeography is the study of the distribution of life over land. Evaluating the presence of fossils of a variety of organisms helps scientists recreate the position of today's continents in the single continent of Pangea.

dideoxynucleotide sequencing

The first DNA sequencing technique used nucleotides that stop PCR• Separating DNA fragments by size indicated the sequence of nucleotides. Dideoxynucleotide sequencing, called Sanger Sequencing, was the first form of DNA sequencing developed. To determine the sequence for a segment of DNA four PCR reactions, each one containing one type of dideoxynucleotide for each of the 4 nucleotides, is prepared. Dideoxynucleotides stop DNA replication because polymerase cannot attach nucleotides to the 3' end of a dideoxynucleotide. For example: A PCR reaction is set up as usual but a small portion of the TTP is substituted with dideoxy TTP (ddTTP) nucleotides. The standard quantity of ATP, GTP, TTP and CTP are used along with all other components of a PCR reaction. While the PCR reaction undergoes the many cycles of amplification a single ddTTP is randomly placed during the elongation step, thus stopping elongation at that point. Over the many cycles a ddTTP nucleotide is placed in each of the possible positions that contains a "T" nucleotide. Keep in mind that PCR results in more than a million pieces of DNA that is typically under 4,000 base pairs, so the odds of a dideoxynucleotide occupying each possible position is quite high. With this method the last nucleotide of a fragment is known, because it must be a dideoxynucleotide, in this case it would be a "T" nucleotide that ended the fragment. This same method is repeated in 3 separate reactions utilizing ddATP, ddGTP, and ddCTP. The PCR samples from each of the four reactions are separated on a gel electrophoresis apparatus that separates the products by size. The gel is "read" from bottom to top (shortest fragment to longest fragment) and the sequence of DNA is assembled. The nucleotide that ends the shortest fragment is the first nucleotide in the sequence, the nucleotide that ends the second shortest fragment is the second nucleotide in the sequence, and so on.This is a time-consuming process that requires computer programs to "reassemble" the DNA sequence. This was the benchmark method used for several decades.

two trait F1 x F1 cross

The individuals in the squares are F2 offspring• The phenotypic ratio is 9:3:3:1. The set-up for the two-trait F1 x F1 cross is the same as it was for the P-generation, but substituting F1 individuals for the Parental individuals. The filled-in squares are the F2 generation, now you can see that the phenotypic ratio of a two-trait cross is more complex than dominant : recessive. For a two-trait cross the phenotypic ratio must capture all four possible phenotypes and is written as this:# dominant 1st trait- : # dominant 1st trait- : # recessive 1st trait- : # recessive 1st trait-dominant 2nd trait recessive 2nd trait dominant 2nd trait recessive 2nd traitThe ratio for the F1 cross initially appeared as 1 Tall-Round : 0 Short-Wrinkled but is actually 1 : 0 : 0 : 0 with all individuals being Tall-Round, none being Tall-Wrinkled, Short-Round, or Short-Wrinkled.The ratio for the F2 cross above is 9 : 3 : 3 : 1. It is expected then that 9/16ths of the offspring will be Tall-Round, 3/16thswill be Tall-Wrinkled, 3/16ths will be Short-Round, and 1/16th will be Short-Wrinkled.If the cross produced 100 offspring, it is expected that:100 x 9/16 = ~56 will be Tall-Round100 x 3/16 = ~19 will be Tall-Wrinkled100 x 3/16 = ~19 will be Short-Round100 x 1/16 = ~6 will be Short-Wrinkled

Multicellullarity

The many different types of cells of multicellular organisms each carry the complete genome of the organism• This has been demonstrated with cloning experiments• The differences in cells is due to the regulation of gene expression in each cell. Multicellularity is a tricky thing. How can billions of cells with the same information be expressed differently in different cells?Gene regulation is responsible for most of the differentiation of cells. Genes are permanently deactivated in cells of different tissues.

Dr. Lenski's Long-Term Experimental Evolution

The mutation that led to the ability to digest Citrate was acquired around the 20,000th generationDr. Lenski at Michigan State began a long-term experiment on E. coli starting in 1988. The experiment began with a single strain of E. coli that was subdivided into 12 populations. Every 24 hours 1% of each of the 12 populations is transferred to a flask of fresh medium and allowed to grow. A 24-hour period represents about 6.67 generation of E. coli. Every 500 transfers a portion of the population is frozen and stored at -80 oC. The culture medium contains the usual supply of bacterial food (glucose) as well as other compounds used to stabilize the medium, one of those compounds is citrate. Recall from cellular respiration that citrate (citric acid) is used in the Citric Acid Cycle and leads to significant ATP production. Wild E. coli cannot utilize citrate as a food source, and neither could the original bacterial strain used in Dr. Lenski's experiment. Around the 33,000thgeneration a flask of E. coli in population #3 was very cloudy and absolutely packed with cells in a much higher concentration ever seen. At first the scientists thought there was contamination of the growth media, and the population was re-grown, with the same results. Analyses show that a new mutation in that population enabled the cells to utilize citrate as a food source, thus supplying more food to the bacteria and causing a population explosion.Going back to the frozen samples, analyses show that the initial mutation that led to the Citrate mutation (Cit+) developed around the 20,000th generation. Multiple mutations accumulated that led to the new ability to metabolize citrate.

History of evolution

The theory of Evolution by Natural Selection was derived from years of varying research. While Charles Darwin is considered the "Father of Evolutionary Theory" he was not the first person to consider the origin of species. In fact, Plato mused about the similarity of species in the 4th century BC. In 1795 Geologist James Hutton suggests the theory of Gradualism. This theory states that changes in nature occur slowly over long periods of time. In 1798 Economist Thomas Robert Malthus published his "Essay on the Principle of Population" that described how populations grow. When given extra food the population will do well until they produce more offspring, increasing the population, and the struggle for food begins again.February 12, 1809, Charles Darwin was born (as was Abraham Lincoln, what a great day!)1809 Jean Baptiste de Lamarck publishes his hypothesis of Evolution by Inheritance Acquired Traits. While his hypothesis was flawed, it provided a starting point for Charles Darwin.1812 Georges Cuvier's work on fossil records is considered the foundation of vertebrate paleontology. Cuvier asserted that extinction is a natural fact. Interestingly, Cuvier was vehemently anti-Evolution, but his work was used to support the Theory.1830 Charles Lyell published Principles of Geology based on ideas from Hutton and from scientific studies. He proposed that the Earth was many millions of years old and incorporated Hutton's theory of Gradualism into his theory of Uniformitarianism. Uniformitarianism states that the same processes witnessed on Earth today are the same processes that occurred in the past. His work allowed for the idea that there has been a long enough span of time during which species could change. Darwin brought a copy of Lyell's book along with him on his world travels (1831-1836) and read it multiple times.After completing his travels Darwin wrote a brief essay about Descent with Modification, Darwin's term for "Evolution". The paper was controversial. Darwin was not interested in causing a controversy, so for many years he simply studied and did his own thing, until Alfred Wallace contacted him in 1858.1858 Alfred Wallace, while studying in the Malay Archipelago, wrote a hypothesis of natural selection. This spurred Darwin to publish his findings in 1859. It has been determined from dates on letters that Darwin did NOT get his ideas from Wallace, rather, both men came to the same conclusion at similar times.1859 Darwin published his book "On the Origin of Species by Natural Selection", in which he never used the word "Evolution". The final sentence of the book reads:"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

Evolution Imperfections

The vertebrate eye has a blind spot where the opticnerve exits the eye• Mollusk eyes have no such blind spot becausephotoreceptor cells are in front of the nerve fibersEvolution does not drive a species towards "perfection", that simply is not possible. Evolution is the result of the selection of individuals that are best suited for an environment at a given time, based on the accumulation of changes in the species. The vertebrate eye is a great example of an imperfect system that resulted from evolution. The vertebrate eye, modified over millions of years, receives light through the eye and then transmits the nerve impulse back towards the front of the eye to nerve fibers that direct nerve impulses to the optic nerve which leaves as a bundle from the back of the eye. This system results in a blind spot where the optic nerve exits the eye. We don't generally notice the blind spot because each eye compensates for the missing information. You can verify this for yourself. Draw a dot about the size of a grain of rice on a white piece of paper, close one eye and look at the dot with the other eye; keep the eye looking forward and slowly move the paper, the dot will completely disappear when it is inline with your optic nerve. Your brain will compensate for the missing information and make the entire paper look white.Mollusk eyes have photoreceptor cells and nerves arranged differently from vertebrate eyes. In the mollusk eye the photoreceptor cells receive light impulses and send the information to the back of the cell out and out the nerve fibers directly to the brain, there is no reflection of light forward. Because there is not an optic nerve that collects information from nerve fibers placed in front of photo receptors there is also no blind spot. The disappearing dot trick won't work with an octopus.What does this mean evolutionarily? It means that these two different eye types most likely diverged long ago when photoreceptor cells and nerve fibers were just beginning to evolve. There were likely other eye variations that arose, but they did not convey enough advantage to persist.

therapeutic cloning

Therapeutic cloning is used for producing cells and tissues rather than entire organisms.Therapeutic cloning is used to generate tissues and organs from cloned cells. Like reproductive cloning, the ideal starting cells are totipotent or pluripotent cells from embryonic stem cells. For the purposes of therapeutic cloning there has been some success with using multipotent cells to produce certain tissue types. One of the goals of therapeutic cloning is to efficiently grow replacement tissues and organs that match the individual and not have complications of rejection.

PCR component- Target Primers

These are short (3-7 nucleotide) fragments of DNA that are used to "target" the region of interest. Primers are commercially available, and made-to-order.

turner and klinefelter syndromes

Turner Syndrome leads to multiple poor health effects• Klinefelter Syndrome frequently goes undiagnosed.Turner Syndrome, Klinefelter Syndrome, and all aneuploid conditions are diagnosed by karyotype. Individuals that experience no effects of their aneuploid condition (Jacobs Syndrome and Triple-X) may never be diagnosed. Where fetal abnormalities are noted, a karyotype is made either via amniocentesis or chorionic villi sampling; in these cases, a karyotype is available before birth.

x-linked pedigrees

Typically "skips" generations• An affected female has an affected father and carrier or affected mother• Affected females will have all affected sons.When evaluating a pedigree chart if many more males than females are affected then it is probably an X-linked trait.While the X-chromosomes carries genes that determine sex, it is a very large chromosome (it is the 8th largest human chromosome) that carries many genes unrelated to sex determination.The X-chromosome carries genes related to red and green color perception, hair retention, and hemophilia -a blood clotting disorder.X-linked characteristics affect males more often• Carriers are unaffected heterozygous females. This is a partial pedigree of the royal families of Europe starting in the mid-1800s. Note that females shaded in purple are "carriers". These women carry the recessive allele but are unaffected because they also carry the dominant, "normal" gene that masks the recessive allele. Carrier women can pass the recessive allele to her offspring, with a 50% chance for each child.Males are more frequently affected by X-linked traits because they carry only one X-chromosome (received from mom) and a Y-chromosome (received from dad) that primarily carries information for how to be male. If a male receives an X-chromosome with a recessive allele, he has no "choice" but to express that allele.Queen Victoria was a carrier for hemophilia, it is unclear where she got the recessive allele from. She had 9 children, 1 son that was affected by hemophilia and 3 daughters who were carriers (determined by their offspring). Notice that the carrier daughters married into other European royal families including Germany, Spain, and Russia, bringing hemophilia to those royal lines. The frequency of affected males increased within the families, in part because of cousin-cousin relations. Note that Alexis in Generation IV was the brother of Anastasia, the Russian princess murdered with her family in the Bolshevik revolution of 1918.

testcross

Used to determine the genotype of an organism with a dominant phenotype• Unknown dominant phenotype individual is mated with an individual with the recessive phenotype.As with the finger length the genotype of individuals with the dominant phenotype is unknown. There are two ways of determining the genotype of an individual with the dominant phenotype. One way is to do a family pedigree to look at what other family members possess as phenotypes and then try to piece together a genotype for the unknown individual. This is typically done with human traits, and for good reason. The other way to determine the genotype of an individual with a dominant phenotype is through a Testcross. In a Testcross the unknown dominant-phenotype individual is bred with an individual with the recessive phenotype. Let's say we have a pea plant that produces dominant Purple flowers, and we want to determine if that plant is homozygous or heterozygous. To do this the unknown genotype Purple-flowered plant is mated with a homozygous-recessive White-flowered plant and the offspring ratio is evaluated.Since there are two possible genotypes of the unknown individual, there are two possible phenotypic ratio outcomes. 1. The plant is Homozygous dominant with a genotype of PP 2. The plant is Heterozygous with a genotype of PpStart by setting up and completing a Punnett square for each possibility.1. PP x pp set up into a Punnett square will result in all offspring with the genotype "Pp" and the phenotype of Purple. The phenotypic ratio is 4:0 (reduced to 1:0) -that is 100% purple.2. Pp x pp set up into a Punnett square will result in half of the offspring with the genotype "Pp" and the other half with genotype "pp". The phenotypic ratio is 2:2 (reduced to 1:1) -that is 50% purple and 50% white.

pedigree analyses

Used to understand patterns of inheritance• Autosomal inheritance-Equal proportion of affected males and females• X-linked inheritance-Disproportionately more affected males. Testcrosses are not done with humans, and there are many times when studying other organisms when a Testcross to determine genotype is impossible or impractical. Pedigree analyses are a tool used to determine the pattern of inheritance for a trait and are used as a diagnostic tool.Genetic Counselors use pedigree analyses to help couples trying to have children determine and understand the risk of genetic disorders of offspring. This is accomplished through tracking family histories of genetic conditions.There are two primary forms of inheritance: Autosomal and X-linked. Autosomal inheritance occurs in traits carried on an autosome, while X-linked inheritance tracks traits carried on the X-chromosome. When evaluating a pedigree, the first step is to determine if males are affected more frequently than females. If there is no difference between the proportion of affected males and females, then the trait carried on an autosome. If more males than females are affected, then the trait is controlled by a gene carried on the X-chromosome.

Galapagos tortoises

Variation within the species is directly related to the habitat of the island the tortoises live on. Galápagos tortoises show adaptations to their local environments as well. Though the tortoises are all the same species there are small modifications based on available food. Some of the islands are relatively flat with low growing vegetation for tortoises eat. Other islands are rockier with shrubs as the primary vegetation.

why dont we do testcrosses with humans?

Well, let's say you have the dominant short finger phenotype. You would have to mate with someone (and have multiple kids with that someone) and the ONLY parameter for that "someone" is that they have the long finger phenotype. Most people would not be willing to partake in that experiment.

single-trait cross

When a single characteristic (e.g.,seed color) is examined in a mating it is called a "Single-Trait cross".

two trait cross

When two characteristics are evaluated at the same time (e.g.,seed color AND plant height) it is called a "Two-Trait cross".

Stem cell persistence

With each round of Mitosis one daughter cells remains as a stem cell -thus maintaining stem cells within the body.Stem cells are persistent and maintained in the body. Each time a stem cell divides one of the daughter cells remains undifferentiated as a stem cell, while the other cell is differentiated int a progenitor cell that begins undergoing differentiation.

epistasis

a gene at one locus affects gene expression at a second locus. epi=above, stasis=equilibrium. Epistasis involves interactions between different genes, where interaction between genes determines the phenotype. Epistasis can be seen in some corn varieties where two separate genes, gene A and gene B, each code for enzymes necessary for color production in the kernel. Corn is white if it is homozygous recessive at either, or both, of these gene locations because the enzyme(s) necessary for pigments are not produced. In the cross shown above each of the P-generation plants produce white kernels for different reasons, one because it is recessive at the B-locus, the other because it is recessive at the A-locus. The F₁ generation produces purple kernels because the individuals carry one dominant allele at each gene locus, thus producing both necessary enzymes for pigment production. The F₂ generation shows a unique ratio of dominant to recessive offspring due to the interaction between the A and B genes. Plants that do not carry at least one dominant allele at each gene locus produces white kernels.

alleles

alternative versions of a gene. Think of a human gene for hair color, each individual carries two genes for this trait "hair color" but the two alleles are likely to be different. One allele may say "black hair" and the other say "brown hair". This is a gross simplification as there are at least 3 genes that control human hair color, but the idea is clear. While some genes have many different alleles, and individuals likely carry two different alleles, there are some genes were most people carry two identical copies of the same allele. For example, recall there is a gene for cytochrome cprotein essential in the electron transport chain in cellular respiration. If an individual didn't have the "normal" copy ofthis gene the fetus would likely not develop. Because there is so much pressure to have a proper protein, we all carry the "correct/normal" gene. And that is good.

F3 generations

are not typically studied but are useful in other applications. F₃ generations are generally not used in breeding studies because the outcome is dependent on which F₂ individuals were used. F₃ plants are used as the start for developing new true-breeding plant lines. Mendel's contemporaries attributed the reappearance of traits to mean that the genetic material was unstable. Thankfully, that isn't the case and Mendel was able to demonstrate how those traits "disappeared".

vestigal structures

are remnant features. Vestigial structures can complicate analyses because they are remnant feature of a shared trait. In the corner of your eye there is a little pink nub with a small flap of pink skin, this is the remnant of your third eyelid! The third eyelid is a homologous structure shared with other organisms but may be overlooked since it is so reduced. The fused human tail bones that make up the coccyx is another example of a vestigial structure. I personally wish I had a tail and a third eye lid. Can you imagine the new expressions we could have. I imagine teenagers would blink their 3rd eye lids at parents.indicate structures that once existed and hint at shared ancestryVestigial structures are structures that have been greatly reduced in some species. For example, manatees, who are related to elephants and African Hyraxes (look them up, they're adorable), still retain "finger" nails on their front flippers. Manatees cannot leave the water and have no function for these remnant nails. In the human body the tailbone, coccyx, is a vestigial tail, while the appendix was likely used by our ancestors to aid in the digestion of tough, fibrous plant material. In your eye there is a vestigial third eyelid; it is found next to the pink "nub" in the corner of your eye. If you look in a mirror and move just your eye to stretch out that inner corner of the eye you can see a small pink "flap" attached to the pink "nub"; that's what's left of your third eyelid. Cats and dogs have retained this third eyelid, also called a nictitating membrane, and is sometimes visible. If you have never seen your pet's third eyelid, gently pry their eye open while they are asleep, you'll be able to see it then. The nictitating membrane is absent from most primates; only lemurs, and some small tree-dwelling primates have retained this feature. It is unclear why the nictitating membrane was lost.

F2 generation

arises from F1 self-pollination. When two F1 individuals are mated, or allowed to self-pollinate, the F2 (2nd Filial) generation is formed. In the case of pea plants, it is a matter of allowing the plants to self-pollinate/fertilize, in animals it would be a brother-sister mating, which some species don't mind at all. Notice that the white flower trait "reappears" in the F2 generation and comprises about 25% of the F₂ population.

Pisum genetic linkage map

as more markers are used in genetic linkage mapping the map becomes more accurate. This is a linkage map of the seven chromosomes of the common pea. It took years to build this map using breeding techniques, DNA biotechnology, and computer programing. Scientists continue to add information to these genetic linkage maps as they collect those data points. Part of my Ph.D. work on Pisum was to add markers to this map. It took years of developing a genetic marker, evaluating the genotype of all the individuals in the study, followed by two years of growing and cross-breeding pea plants and another year of completing computer programming for and statistical analyses of genetic linkage maps.

nondisjunction

can occur in either meiosis 1 or 2. Nondisjunction results in aneuploid gametes. A Karyotype can diagnose changes in individual chromosomes as well as diagnose abnormal chromosome numbers. An individual with the usual number of chromosomes is termed euploid(eu=true, ploid=chromosome number) while individuals with an abnormal number of chromosomes are termed aneuploid (an= not, eu=true, ploid=chromosome number). Aneuploidy arises through incorrect division of genetic material during Meiosis. This incorrect division is called nondisjunction (non=not/didn't, dis = apart, junction = two things that are together). Therefore, nondisjunction means "two things that came together, were supposed to come apart, but didn't".Nondisjunction events occur in Meiosis I or Meiosis II. If nondisjunction occurs during separation of homologous chromosomes in Meiosis I all four resulting gametes will be abnormal, either with an extra chromosome, or lacking a chromosome. If the nondisjunction occurs during separation of sister chromatids in Meiosis II, two normal gametes and two abnormal gametes are formed.The image above shows nondisjunction events occurring in the formation of egg gametes. Studies show that nondisjunction occurs more frequently in egg formation. The prevailing hypothesis as to why nondisjunction occurs more commonly in the egg cell is because of the long delay between Meiosis I and Meiosis II. Recall that egg cells only undergo Meiosis II when fertilization occurs; this may be 30, 40, even 50 years after Meiosis I occurred.The image above only shows the abnormal chromosomes; all the other chromosomes in the cell complete Meiosis as expected.Assuming these eggs are fertilized by chromosomally normal sperm the results are euploid (2n) offspring, and aneuploid (2n+1 or 2n-1) offspring.

fetal testing

cell-free fetal DNA tests are new, non-invasive method.There are three primary types of pre-natal testing for genetic abnormalities. (a) Amniocentesis is the extraction of a portion of the amniotic fluid that surrounds the fetus. A large needle is guided through the mother's abdomen and uterus wall using ultrasound images to guide the needle. A few milliliters of fluid carrying sloughed off fetal cells are extracted. The cells are cultured in a laboratory and analyzed by karyotype. This procedure is generally performed between 18-22 weeks gestation and carries a 2% risk of miscarriage. I had amniocentesis done with my second child. Not a comfortable procedure, to say the least. (b) Chorionic Villi Sampling (CVS) removes a small sample of cells from the placenta (the placenta is derived from the fetus). The cells are removed by going through the cervix with a probe that removes a small bit of tissue. That tissue is cultured in a lab and cells are used to produce a karyotype. This procedure is performed between 12-16 weeks gestation and carries a 4% risk of miscarriage. (c) Non-Invasive Prenatal Testing (not shown) is a blood test that extracts the small amount of fetal DNA found in a mother's blood stream and analyzes that DNA for common chromosomal abnormalities. The test is sensitive enough to determine gender of the fetus and distinguishes between the current pregnancy and previous pregnancies. This procedure is generally performed between 9-12 weeks gestation and carries 0% risk of miscarriage but cannot detect as many abnormalities as amniocentesis or CVS. I had this done with my 3rd kid; it was a much more pleasant procedure.

Evolution

change in species over time

restriction endonucleases

cut DNA at specific nucleotide sequences. Restriction endonucleases are used to cut DNA molecules into smaller fragments. Some endonucleases make "blunt cuts" that result in DNA fragments with no un-paired nucleotides at the cut site. Other endonucleases form "sticky ends" on DNA fragments where un-paired nucleotides remain at the ends of the fragments. Restriction endonucleases recognize a particular DNA sequence called a restriction site. In the example above the restriction site contains the sequence 5' GAATTC 3'; the restriction enzyme cuts between that G and A and results in a "sticky" overhang of 5' AATT 3'. The sticky ends readily bind with the same sequence on another molecule. DNA ligase is used to join the sugar-phosphate backbone of the newly joined fragments.

autosomal recessive

cystic fibrosis, sickle cell-anemia.In all Pedigree charts males are represented as squares and females are represented as circles. Affected individuals are shaded and unaffected individuals are not. In the pedigree above there are 2 affected females and 1 affected male so this is an autosomal condition. The alternative, an X-linked pedigree, would show many more affected males than females.With autosomal conditions there are autosomal recessive and autosomal dominant inheritance. Autosomal recessive inheritance means that affected individuals carry 2 recessive alleles. Autosomal recessive conditions may "disappear" for a generation or two, then reappear in a family.Note that generations are noted with Roman numerals, with the youngest generation at the bottom, with the largest Roman numeral.The pedigree above shows an affected woman mated (not necessarily married) a man who is unaffected. They have two unaffected daughters (oldest offspring is leftmost, youngest is rightmost). All that is known of the I Generation male is that he must carry one dominant allele since he is unaffected. The male's second allele cannot be determined. The Generation II daughters must be heterozygous because they have the unaffected phenotypes, but their affected mother must have passed a recessive allele to each daughter. These two daughters each mate with unaffected males (again, the full genotype of the males cannot be determined) and have children of Generation III. The genotypes of the Generation III individuals that had offspring can be determined because of their children. The two remaining Generation III individuals have unknown genotypes beyond carrying one dominant allele and being unaffected. Note the double horizontal line between two Generation III individuals -this indicates inbreeding, in this case 1st cousins, a genetic "no-no". Two of the Generation IV offspring are affected, which means each of their parents must carry a recessive allele; this provides the information necessary to determine their parent's genotypes. The unaffected Generation IV daughter again has an unknown genotype.In autosomal recessive traits affected individuals can have unaffected parents. Cystic fibrosis and Sickle-cell disease are both examples of autosomal recessive traits, there are many more.

Setting Up a Punnett Square

each filled-in square must include the offspring genotype and phenotype.The gametes each parent forms are lined up along the left side and the top. Be sure to place all the gametes one parent can produce on each side, don't mix gametes.Match the gametes together to and place them in the squares. Match gametes by rows and columns. The top-most gamete of parent 1 is placed in the boxes to the right of the gamete while the gametes from parent 2 are written in the boxes below the gamete. Always place the upper-case dominant letter (if present) in front of the lower-case recessive letter (if present), regardless of which parent the dominant allele came from.The offspring in the Punnett Square are the F1 generation. Include the genotype and phenotype for each F1 offspring within the box.

PCR component- Template DNA

extracted from cells of the study organism. The extracted DNA must be high quality and high concentration to be used successfully.

Who was Gregor Mendel?

father of genetics.(1822-1884) was an interesting man trained in mathematics, statistics, and natural sciences. Mendel was curious about how parents passed information to their offspring. Essentially, how do zebras always make baby zebras and never a horse or donkey? Mendel worked with several different species (he was an intense bee-keeper) before settling on Pea plants as his model organism. Keep in mind that as Mendel was trying to answer his question about inheritance, there was scientists had not yet discovered DNA. He sought to answer his question while missing information that would have made his quest much simpler. In the end Mendel collected thousands of pieces of data and found an answer to his question. While he attempted to share his research, he was met with only mild interest, and did not pursue academic recognition. Mendel stored his research and later died. It wasn't until the early 1900s that his works were re-discovered and evaluated. It is known that some of his research journals were lost in a fire after his death.Trained in Natural Sciences and Mathematics Gregor Mendel devoted his life to understanding inheritance.

meiosis

formation of gametes. a diploid organism with two copies of each chromosome will produce haploid gametes that each contain only one copy of each chromosome.

when is an individual described as homozygous

if they carry two identical alleles at a gene location. Consider the cytochrome cgene, most humans are homozygous for the "normal" version of the gene.It is difficult to obtain completely homozygous individuals (especially with animals because there would have to be some disturbing breeding practices) but some plants can be forced to homozygosity through continued inbreeding. Pea plants, since they self-pollinate, tend to be very homozygous, which is very convenient for genetic studies.

when is the initial cross completed

in the parent (P) generation.In genetic crosses the first two individuals used to start a new line are called the P generation individuals. In the case of the pea plants the P generation plants were true-breeding, meaning the purple-flowered plant only ever produced offspring with purple flowers and the white-flowered plant only ever produced offspring with white flowers.

recombinant molecules

inserting DNA into a plasmid generates a recombinant DNA molecule. Recombinant DNA molecules are molecules that contain DNA from two, or more, different organismal sources. Bacterial plasmids are typically used in the formation of recombinant DNA molecules because they are small and easily manipulated in a laboratory. A plasmid carrying an antibiotic resistance gene is cut with a restriction enzyme to create sticky ends. The foreign DNA is cut with the same restriction enzyme so that the sticky ends match, thus facilitating the insertion of the foreign DNA into the plasmid. The new, recombinant plasmid is inserted into bacteria which are then "screened" using an antibiotic. The bacterial cells that took up the plasmid, with the antibiotic resistance gene, survive in the presence of the antibiotic. Bacterial cells that did not take up a plasmid die in the presence of the antibiotic. In this way, researchers can grow and cultivate only bacteria that carry the recombinant molecule.

DNA library

is a set of bacteria that contain all the DNA fragments from an organism. a DNA library represents the entire genome of an organism. To produce a DNA library DNA is extracted from a source organism, fragmented, and inserted into plasmid vectors. The plasmid vectors are taken up by bacterial cells through the process of transformation. Each bacterial cell, and its descendants, carry a fragment of the source DNA genome; all the bacterial cells combined represent all the DNA from the source organism. A DNA library then is maintained through the propagation and maintenance of bacterial cells.

descent with modification

is complicated by missing link species.Descent with modification is clearly visible in the evolution of the modern-day horse, Equus. The horse evolutionary lineage has one of the most complete sets of available fossils, but there are still missing links. Through evolution of the modern-day horse there were changes in body size, toe count, and tooth size and shape. Generally, the body size increased over time, though there was a reduction with Nannippus. Over time the four fleshy toes were reduced to a bony hoof with fusion and reduction of toes to the single bony hoof of the modern horse. Overall teeth size became larger along with the body, but also are better suited to the grazing behavior and grinding tough grass. This Evolutionary tree is truly more of an evolutionary "bush" as there are multiple branches each leading to more branches.

cDNA

is formed from mRNA using reverse transcription. cDNA represents DNA fragments that are likely protein-coding regions. cDNA (complementary DNA) is produced by reverse transcription of mRNA sequences. mRNA is extracted from cells during specific developmental phases, or from cells that behave in a particular manner. The mRNA is then treated with the enzyme Reverse transcriptase that produces DNA from RNA (opposite action from RNA polymerase). The single-stranded DNA that results is treated with DNA polymerase to form double-stranded DNA. The newly formed cDNA lacks introns and represents a protein-coding DNA segment. The protein that is formed by this DNA fragment is not known until further studies are completed.

genotype

is the alleles carried by an individual; it is expressed as either letters or as a description like "homozygous dominant".

phenotype

is the outward appearance of an individual; it is expressed with words like "tall", "purple-flowered", "wrinkled seeds"

polygenic inheritance

many traits are controlled by multiple genes. Traits controlled by polygenic inheritance display a characteristic bell-shaped curve when graphed. Polygenic (poly = many, genic = genes) traits are traits controlled by many genes and they are common. A trait is determined to be polygenic by looking at the phenotypic distribution. For example, human height is a polygenic trait easily detected by lining up a group of people from shortest to tallest. Humans aren't "tall" or "short" like pea plants, there is a wide range of heights. A graph of the number of people at each height would reveal a bell-shaped curve with most adult humans between 5'3" and 6'0".. ex with wheat seed variation. The example above is of wheat seed color variation. It is known that this trait is controlled by 3 genes, each with a dominant and recessive allele. Think of each dominant allele as a "drop of color". A plant with 6 recessive alleles (aabbcc) will have white seeds while a plant with 6 dominant alleles (AABBCC) will have dark red seeds. White and dark red are less common in a population because each can be achieved with only one genotype: aabbcc or AABBCC. A mating between a white-seed individual and a dark red-seed individual produces F1offspring with medium-red seeds (AaBbCc). All seven possible colors are apparent in the F2 generation, but all colors are not seen equally. Only 1 in 64 individuals will be either white-seeded or dark-red seeded. Medium-red seeds will be the most common phenotype (20 of 64 individuals) because medium-red seeds occur by having any three dominant alleles. A plant with medium red seeds could have the genotype: AaBbCc, AABbcc, aaBBCc, aaBbCC, and so on.

PCR component- H2O

may be added to create an aqueous environment. Some commercial preparations of Buffer, dNTPs, or Polymerase have the water already added to an appropriate concentration.

which of mendels laws describes gamete formation

mendels principle of segregation and independent assortment describe gamete formation.

sex determination

not the same for all organisms.Sex determination in Mammals and some insects follows the familiar X-Y system shown in the fruit fly crosses. Individuals with 2 X-chromosomes are female. The Y-chromosome provides information to make the male body. Individuals with a malfunctioning Y-chromosome will be born female due to the single functioning X-chromosome. Sex of the offspring is determined by the X- or Y-chromosome provided by the male parent.The X-O system, used by spiders, grasshoppers, dragon/damselflies, some worms, and some mollusks produce female offspring with 2 X-chromosomes and male offspring with 1 X-chromosome. There is no sex-determining chromosome, rather it is the number of X-chromosomes that determine sex.Birds, some reptiles, and some insect use the Z-W system where individuals with 1 Z- and 1 W-chromosome are female, while individuals with 2 Z-chromosomes are male. Sex of the offspring is determined by the gamete provided by the female parent, opposite of the X-Y system.The haplo-diploid system of sex determination is found in the Orders Hymenoptera (bees, ants, and wasps), Thysanoptera ('thrips'), and sporadically in some other insect species. In the haplo-diploid system diploid individuals are female and haploid individuals are male. The diploid queen lays haploid eggs, if the eggs are fertilized by a haploid male drone (gametes produced through Mitosis, not Meiosis) then diploid female offspring result. If the haploid eggs remain unfertilized, they develop into haploid males.A quick note on the terms sex and gender. Sex is defined by biology, the condition of an individual's chromosomes. Gender is a social construct that attempts to define how individuals should behave within their sex.

Turner Syndrome

noted 45; XO occurs when an individual carries one X-chromosome and no second sex chromosome. Turner syndrome occurs 1 in every 2,000-4,000 live births. These individuals are born female but do not fully develop female characteristics and are sterile in adulthood. Individuals are typically shorter in stature with a wider base of the neck; learning impairments may also occur.

Klinefelter syndrome

noted 47, XXY occurs 1 in every 500-600 live births. These individuals have typical male anatomy but have longer-than-usual limbs and do not grow significant face or body hair. Klinefelter males typically experience learning disabilities and are sterile in adulthood. Microscopic analysis of cells would show that these males carry a Barr body in each cell while euploid males carry no Barr bodies. Most Klinefelter males go undiagnosed.

genomic imprinting

occurs when a condition is expressed only when it is carried on one parental chromosome but not the other.Genomic imprinting is demonstrated in phenotypes that differ based on which parental chromosome is inherited, not necessarily on the genotype of the individual. Dwarfism in mice is transmitted by the paternal chromosomes, not the maternal chromosomes. Mating between normal-size and dwarf mice gives normal-size or dwarf offspring depending on which parent was the dwarf parent. When the dwarf mouse parent is the mother, offspring are heterozygous and normal-size. When the dwarf mouse parent is the father, offspring are heterozygous and dwarf. Note that the offspring have the same genotype (heterozygous) but have different phenotypes.In humans, Prader-Willi and Angelman syndromes are both caused by a small deletion in chromosome 15. Prader-Willi Syndrome leads to respiratory distress, obesity, short stature, mild mental retardation, and obsessive-compulsive behavior. Angelman Syndrome leads to developmental delay, severe mental retardation, hyperactivity, aggressive behavior, and inappropriate laughter. If the chromosome with the deletion is inherited from the father Prader-Willi Syndrome occurs, if the chromosome with the deletion is maternally inherited Angelman Syndrome occurs.

autosomal dominant.

osteogenesis imperfecta, achondroplasia dwarfism. In this pedigree there are 3 affected males and 3 affected females, thus leading to the conclusion that this must also be an autosomal condition. In this case the condition is Autosomal Dominant, meaning the presence of a dominant allele causes the condition. Achondroplasia dwarfism is an example of an autosomal dominant condition. Individuals who have achondroplasia dwarfism must carry one, or more, dominant alleles. Everyone that does not have achondroplasia dwarfism is homozygous recessive for the condition. Osteogenesis imperfecta is also called "brittle bone" disease; slight impacts to the bone result in breaks. Children with osteogenesis imperfecta typically break hundreds of bones in childhood alone.In the family pedigree above two affected individuals have 4 offspring (1 son followed by 3 daughters). The Generation I individuals must have been heterozygous because they have 2 unaffected children, daughters in this case, who are homozygous recessive. In order to have homozygous recessive offspring each parent must have donated a recessive allele. The Generation II male mates with an unaffected woman and they have 3 children, two of which are affected. One of the unaffected Generation II females mated with an unaffected male and therefore have all unaffected offspring; this branch of the family will no longer carry the condition, unless an affected individual enters the family branch.Notice the pattern that every affected individual must have an affected parent.

multipotent cells

partially differentiated. have had significant differentiation but can still differentiate more. Bone marrow cells, for example, can become any type of blood cell, but they can't become a liver cell.

common human conditions

recessive and dominant conditions are found in the human population. these conditions can be tracked by pedigree analyses.

genetic linkage mapping

recombination frequency (%) is equal to distance between genes recorded as map units. Genetic linkage mapping uses recombination frequency data to construct a map of chromosomes.The recombination frequency is converted to an arbitrary unit called a map unit. Many breeding experiments evaluating recombination between different traits are compiled to create a Genetic Linkage Map. The more experiments completed, and the more data gathered increases certainty of recombination frequency and map unit distances.Map units are given the unit centi-Morgans (cM) in honor of Dr. Morgan. One cM is equal to 1% recombination frequency. Map unit (cM) distances cannot be compared between species. That is 1 cM in one species is a different physical length from 1 cM in another species.

homologous structures

represent variations on a structure present in a common ancestor.These represent two different evolutionary lineages leading to organisms with homologous eye structure due to shared ancestry.

phenotypic ratio

s the eventual "answer" to a Punnett square problem. Phenotypic ratios are always expressed as:Number of Dominant Phenotype Offspring : The Number of Recessive Phenotype Offspring

Bioremediation

s the use of GMO organisms to help restore damaged ecosystems.Genetically modified bacteria have been produced to breakdown oil residues after an oil spill. As well, plastic-eating bacteria have been discovered and are the source of current research to address the global plastic pollution problem.

gel electrophoresis

separates DNA fragments by size. Gel electrophoresis is a process by which DNA fragments are separated by size. The first gel electrophoresis applications used DNA fragments that resulted from restriction enzyme digestion. DNA is treated with different restriction endonucleases in different reaction tubes. The different restriction endonucleases cut the DNA in different locations, forming different DNA fragment lengths. The digested DNA is separated on an agarose gel that allows smaller DNA fragments to move farther than larger DNA fragments. Due to the phosphate groups in the sugar-phosphate backbone, DNA is naturally negatively charged. Gel electrophoresis applies an electrical charge across the gel matrix, drawing DNA towards the positive anode end of the gel. Smaller DNA fragments move through the gel matrix more quickly, thus moving farther in the gel. The DNA in the gel is stained and visualized. In the example above the same DNA is digested in three different reaction tubes using three different restriction enzymes. Looking at the results in the gel gives an idea of where each restriction enzyme site is on the DNA. With enough data a restriction "map" of DNA can be produced.

homology

similarity due to common ancestry. Amphibians, Reptiles, Birds, and Mammals all have simple eyes with a single lens.• All Insects and some crustaceans have compound eyes with multiple lenses.

Pluripotent Cells

slightly undifferentiated (cannot form placenta). have undergone some differentiation already; that is some genes have already been permanently turned off or on. These cells can not form a placenta.

multiple alleles and codominance

some genes have more than two alleles. two dominant alleles will both be expressed. Not all traits come in two "flavors" of alleles (tall vs short, purple vs white, etc.), this is the concept of multiple alleles.As well, if multiple dominant alleles exist then Codominance (shared dominance) is expressed.Human blood type is a great example of multiple alleles and codominance.In the human population there are three alleles for blood type, hence multiple alleles. There are two dominant alleles, IA and IB. Each of these codes for the production of a carbohydrate on the surface of a red blood cell. Those carbohydrates are slightly different from each other and are symbolized as a triangle (A) or a circle (B). The third allele is a recessive allele that does not code for any carbohydrate on the surface of the red blood cell. The recessive allele is noted as a lower-case "i".Note: The letter "I" is used in this case to represent Immunoglobulin, the anti-body proteins present in blood.The three different blood-type alleles produce four different Phenotypes (blood types): Type-A, Type-B, Type-AB, and Type-O.Individuals that have Type-A or Type-B blood are either homozygous for the dominant allele (IAIA or IBIB) or are heterozygous (I^Ai or I^Bi).Type-AB blood only comes from having both the dominant A allele AND the dominant B allele (I^AI^B). These alleles are both expressed -This is codominance.Individuals who are homozygous recessive (ii) have Type-O blood. The Rh factor (positive or negative blood) is a separate gene with only two alleles (dominant positive and recessive negative). "Positive" blood is positive for the presence of the Rh factor carbohydrate on the surface of the blood cell, "negative" blood lacks thecarbohydrate. An individual with positive blood has the genotype RR or Rr, while negative blood type has a genotype of rr. To express an individual's full blood type four alleles are displayed.An individual that has A+ blood would have one of the following genotypes: I^AI^ARR, I^AI^ARr, I^AiRR, or IAiRrAn individual with AB- blood has the genotype: I^AI^Brr A two-trait Punnett square can be made to determine the possible blood types of the children that result from a mating.

environment and phenotype

sone phenotypes are affected by the environment the individual is exposed to. The environment that an organism grows in can have a dramatic effect on the phenotype of the organism. Hydrangeas have completely different flower colors based on the pH of the soil they are grown in. One could dig up a pink-flowered hydrangea and replant it in acidic soil to get blue flowers the next growing season.Consider human height again, if two identical twins (exact same DNA) were separated at birth and raised in different environments is it expected they would be the same height at 25 years old? It is expected that there will be slight variations due to childhood-illnesses, access to medicine, quality of nutrition, etc. There have been many fascinating identical twin studies, but a photographic study recently gained quite a bit of attention. The study involved identical twins with different smoking habits; the twin that smoked, or smoked longer, shows significantly more changes to the skin and generally looks older.

F1 x F1 X-linked punnett square

the 3:1 ratio is ecident but now there is an explanation for why only males are white-eyed. Using Sex-linkage as the mode of inheritance, the expectation that all white-eyed F₂ flies are male is demonstrated in this Punnett Square.From this cross only males can be white-eyed. If a different cross had been set up, white-eyed females are possible.In order to get white-eyed females the mother must be either a heterozygous carrier (XRXr) or be white-eyed (XrXr). The father must be white-eyed (XrY). Try setting up and drawing out a Punnett square for the following cross: Heterozygous red-eyed female (XRXr) mated with a white-eyed male (XrY).

polymerase chain reaction

the backbone of biotechnology. PCR is used to produce millions of copies of a particular DNA sequence; this is referred to as amplifying DNA. PCR is carried out in a 0.2 ml reaction tube and requires specific components in order to run correctly. Components of the PCR reaction: template dna., dNTPs, Taq Polymerase, target primers, MgCl2 buffer, H20.

Agglutination

the clumping of red blood cells in response to antigen presence.

F1 generation

the first generation of offspring obtained from an experimental cross of two organisms. The offspring from the P x P breeding are the F1 (1st Filial -Family) generation. An F1 individual carries 50% of the genes from each parent. In the example above the white flower trait seems to have "disappeared" in the F1 generation.

different alleles

the genetic make up of an individual is expressed using letters to represent the alleles that individual carries. Upper-case letters indicate that an allele is dominant while lower-case letters indicate an allele is recessive. The letter used really doesn't matter, but letters that can be easily distinguished between upper and lower case must be used. To this end, it is recommended that you do NOT use: c, k, m, o, s, u, v, w, x, z to represent alleles.

human chromosome mapping

the human x-chromosome carries 1,805 genes -821 genes have known mutant alleles -59 diseases have been linked to these mutant allels. Human chromosome maps have been determined and revised over the previous decades. CHromosome maps are used for determining where genes related to disease are located; a first step in understanding and preventing genetic diseases.

down syndrome- trisomy 21

the most common human aneuploid condition. Down syndrome is the most common aneuploid human condition, occurring in about 1 in 700 births. The karyotype shows the presence of a 3rd copy of chromosome 21. Individuals with Down Syndrome (named for Dr. Down) have a short stature, short fingers and toes, flat face with a particular fold in the eyelid. Mental retardation from mild to severe is common as are developmental delays in walking and talking. Great strides in medical care have extended the life span of individuals with Down Syndrome from about 25 to 60.Other autosomal trisomy conditions seen include:Warkany Syndrome 2 - Trisomy 8 (rarely survive to birth)Trisomy 9 -rarely survive to birthPatau Syndrome -Trisomy 13 (~1 in 10,000-25,000 births, median survival is 12.5 days)Edward Syndrome -Trisomy 18 (~1 in 5,000 births, median survival is 5-15 days)Trisomy 22 -rarely survive to birthThese trisomies occur infrequently but individuals born with other autosomal Trisomy conditions are never seen. Does that mean other autosomal trisomies don't happen? No, it means they are not survivable through embryonic development. It is suggested that these other autosomal trisomy conditions are so incompatible with life they result in miscarriages before diagnosis. In the world of genetics, more is very bad.

x-linked punnett square

the principles of the punnett square are the same. the ratio must be given by sex though. Punnett Square set up for the white-eyed male fly mated with a homozygous dominant red-eyed female testing if the eye color trait is sex linked.The ratio of the offspring must be given by sex when sex-linked traits are examined. For the example above the ratio would be written as -Female - 1 : 0 Male - 1 : 0 The F1 x F1 cross is set up like this: F1-Generation: Parent 1 Parent 2 Phenotype: Red ♀ Red ♂ Genotype: XRXr XRY Gametes: XR and Xr XR

natural selection

the process that drives evolution.

homologous chromosomes

the two copies of a chromosome carried by a diploid organism. The two copies of the chromosomes are similar, but not identical. They are similar in that they carry the same genes in the same location. (homo=same, logus=location) but the genes at those locations may be slightly different.

using the y-chromosome

the y-chromosome has been used to trace ancient human migration patterns and establish lineages. The Lemba people of southern Africa (sometimes referred to as "Africa's Jews") have a long oral history recounting the tale of their how they are the descendants of Moses' brother Aaron. The Cohanim Jews are descendants of the original Jewish Priesthood and have a written history of their ancestry. Through Y-chromosome DNA studies it has been shown that the Lemba men carry a Y-chromosome that is most like the Y-chromosome of men of Middle Eastern descent and shares identical regions of the Y-chromosome carried by modern-day Cohanim Jews. This finding helps reinforce the oral history of Lemba.Y-chromosome analyses are used to trace human migration patterns like studies of maternally-inherited mtDNA. Back on Slide 4 it was suggested that you should try setting up the following fruit fly cross: Heterozygous red-eyed female (XRXr) mated with a white-eyed male (XrY)The phenotypic ratio of the offspring is: Female -1 :1 and Male -1:1.

PCR component- dNTPs

this is a commercially available micture of triphosphate nucleotides, ATP, TTP,CTP, and GTP. these nucleotides are used to build new DNA strands. The nucleotides are in the triphosphate form so that there is energy available to promote the reaction. Recall that energy is stored in phosphate bonds.

PCR component- Taq polymerase

this is a commercially available, heat-stable DNA polymerase derived from Thermus aquaticus, a bacteria found in a hot spring in Yellowstone National Park. Taq Polymerase assembles new DNA molecules under proper conditions.

PCR component- MgCl2 buffer

this is a salt buffer used to form an electrically-favorable environment

Totipotent Cells

undifferentiated. have all genes available to be activated, with the proper signals. These cells could develop an entire individual.

Reverse Transcription- PCR

used to determine when genes are active in cells. utilizes mRNA as the starting molecule. Reverse Transcription produces cDNA. Target sequences in the cDNA library are then amplified by PCR. In this case, the expression of a protein is analyzed in different embryonic stages. In stage 1 there was no expression of the gene, small expression in stage 2, and similarly high levels of expression in all subsequent stages. This type of data helps inform researchers about the purpose of a gene.

sex-linkage

white-eyed fruit flies carry a mutation on the x-chromosome. Thomas Hunt Morgan (1866-1945) was a prominent geneticist who was awarded the Nobel prize for physiology and medicine in 1933 for his work on chromosomal inheritance. Morgan's laboratory worked extensively with Drosophila, commonly called fruit flies. Wild-type fruit flies, like what show up when your bananas are over ripe, have red eyes. One day a graduate student in Morgan's lab discovered a white-eyed male fly. This was a random, spontaneous mutation in the fruit fly population. The mutation was of great importance and that fly was used in extensive genetic crosses to determine how the white-eyed trait transmitted.The white-eyed male was mated with a homozygous red-eyed female; all the offspring were red-eyed which means that red is dominant to white. The heterozygous F1 offspring were mated and the F2 generation produced a predictable 3:1 ratio of red-eyed : white-eyed flies with one significant exception. All white-eyed flies were male. Statistically, half of the white-eyed flies should be female, but all the white-eyed flies were male; this was a significant finding.With this data it was determined that the eye color gene must be located on the sex-determining chromosome (we'll call it X for simplicity). The Drosophila eye color gene has two alleles: dominant red and recessive white.Notation for sex-linked traits use an "X" with the allele indicated as a superscript, like this: XR = red allele on the X-chromosome, Xr = white allele on the X-chromosome. Every female carries 2 X-chromosomes, and each male carries 1 X-and 1 Y-chromosome. The Y-chromosome carries a handful of genes used for male body formation and carries no genes for eye color. A red-eyed female has the genotype XRXR or XRXr, a red-eyed male has the genotype XRY. A white-eyed female has the genotype XrXr and a white-eyed male has the genotype XrY.A white-eyed male mated with A homozygous red-eyed female is set up like this: P-Generation: Parent 1 Parent 2 Phenotype: Red ♀ White ♂ Genotype: XRXR XrY Gametes: XR Xr and Y

dominant alleles

will mask the presence of a recessive allele. not necessarily the "normal" or "common" allele, they simply cover the presence of a recessive allele. From the previous slide we now know that the purple flower color must be dominant to the white flower color; that's why white seemed to "disappear" in the F1 generation, it was simply being masked by the purple allele.