Final draft Essay 3

Influential factors for evolution: Environment, Mutations and Inheritance

Long before the science of genetics formally began with the great work of Mendel, many intellectuals wondered about patterns of similarities seen in nature. Scientists observed that there were certain resemblances among groups of organisms, but there was a common belief that all beings were made by God, and that He brought them to Earth the way they are today.  People believed that God’s creations were perfect, and that they would never change from the original form designed by the Creator.  The theory of evolution brought great controversy to this belief.  Evolution refers to the genetic changes in a population that can lead to the development of new species throughout time.  This major scientific theory explained to those, who were searching for answers, why there were groups of organisms that looked alike.  The theory of evolution provided a mechanism that demonstrated how the species changed.  Environment, mutations and inheritance are factors that drive natural selection and other evolutionary forces to cause evolution.

For each species there is a proper habitat.  The space, or niche in which species live, contains favorable conditions that allows them to survive.  All of the organisms living within such space are adapted to the conditions that are present there, i.e. temperature, light, nutrients (Pidwirny, M.).  For instance, the point of reproduction for a species of birds, the great tits, is affected by the change in temperature. If the temperature is too cold, it causes the birds to lay the eggs earlier, but if the conditions are too warm, it causes them to delay laying eggs (Visser et. al).  Changes that occur in conditions favorable for a certain species can greatly affect the way it develops.  Constant adaptation to these changes in the environment is critical for the survival of a species.  The great 19^th century naturalist, Charles Darwin, in his book The Origin of Species wrote: “As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form” (5).

Although Darwin did not know much about the mechanisms of inheritance, in his studies, he observed that certain characteristics were more frequent than others.  In order for new characteristics to appear, genetics changes, known as mutations, must occur first.  There are always some mutations arising, so the genetic material is constantly provided with variation.  Genetic changes are critical for the propagation of species: a species must be variable to adapt to the fluctuations in the environment.  The frequency of mutations that accumulate in a species is a key factor that determines the rate by which the species is adapting and therefore evolving (Stebbins and Ayala).  A species that contains the same genetic material for many generations will most likely become extinct, since its gene variants may no longer be favored by the new environmental conditions.  One of the leading evolutionary biologists of the 20^th century, G.L. Stebbins, along with Professor Francisco J. Ayala of the University of California point out the importance of mutations in an evolutionary aspect: “Genetic changes underlie the evolution of organisms; mutations are the ultimate source of the genetic variation that makes possible the evolutionary process” (967).

Mutations that occur in genes create new forms called alleles. These new forms are passed down through generations.  Most new alleles carry detrimental effects, but the inheritance of some new alleles can benefit survival of the species.  For example, research showed that 46,880 years ago dogs carried a mutation for black coat color and recently, scientists have found that wolves that live in forested areas inherited the allele from interbreeding with dogs (Anderson et al.).  Acquiring this melanistic allele benefited wolves who hunted in dark forests.  Dr. Anderson from Stanford University addresses the benefit of melanism in wolves:  “The potential selective value of dark versus light coat color has been suggested to include concealment during predation and/or indirect effects due to pleiotropy, but remains unresolved because the underlying gene(s) have not been identified”.  The inheritance of black coat allele has propagated quickly in wolf populations across North America.  Natural selection increased the frequency of the allele, but the value of this adaptation is still not well understood (Anderson et al.).

The environment provides the pressure on the genetic material (the DNA), and during cellular division, mistakes happen in DNA replication (mutations).  These mutations can be passed on to the next generation (inheritance).  While some of them are harmful, others can provide advantages and increase survival and reproduction of the species (selection).  Natural selection works on mutations that already exist in the population.  Evolution occurs when mutations are selected and passed on through generations.

Work Cited

Anderson, T. M., et al. "Molecular and Evolutionary History of Melanism in North American Gray Wolves." Science 323.5919 (2009): 1339-43.

Pidwirny, M. (2006). "Concept of Ecological Niche". Fundamentals of Physical Geography, 2nd Edition. Date Viewed. http://www.physicalgeography.net/fundamentals/9g.html

Stebbins, G. L., and F. J. Ayala. "Is a New Evolutionary Synthesis Necessary?" Science 213.4511 (1981): 967-71.

Visser, M. E., L. J.M. Holleman, and S. P. Caro. "Temperature Has a Causal Effect on Avian Timing of Reproduction." Proceedings of the Royal Society B: Biological Sciences 276.1665 (2009): 2323-331. Print

Draft Essay3 Influential Changes: Environment, Mutation and Inheritance

Influential changes: Environment, Mutations and Inheritance

Long before the science of genetics formally began with the great work of Mendel, many intellectuals began wondering about patterns of similarities observed in nature. Scientists observed that there were similarities among groups of organisms, but there was a common belief that all organisms were created by God, and that He brought them to Earth the way they are today.  People believed that God’s creations were perfect, and that they would never change from the original form designed by the Creator.  The theory of evolution brought great controversy to this belief.  Evolution refers to the genetic changes in a population that, can lead to the development of new species throughout time.  This major scientific theory explained to many scientists, who were searching for answers, why there were groups of organisms that looked alike.  The theory of evolution provided a mechanism that demonstrated how the species changed.  Environment, mutations and inheritance are factors that drive natural selection and other evolutionary forces to cause evolution.

For each species there is a proper habitat.  The space, or niche in which species live, contain favorable conditions that allows them to survive.  All of the organisms living in that space are adapted to the conditions that are present, i.e. temperature, light, nutrients (Pidwirny, M.).  For instance, the point of reproduction for a species of birds known as the great tits is affected by the changes in temperature. If the temperature is to cold, it causes the birds to lay the eggs earlier but if the conditions are to warm then it causes a delay in laying eggs (Visser et. al).  Changes that occur in conditions that are favorable for a certain species can affect greatly how it develops. Adapting to the changes in environment is critical for the survival of a species.  The great 19^th century naturalist, Charles Darwin in his book The Origin of Species wrote: “As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form.”(page 5)

Although Darwin did not know much about the mechanisms of inheritance, in his studies he observed that certain characteristics were more frequent than others.  In order for new characteristics to occur genetics changes known as mutations must occur.  There are always some mutations occurring, so the genetic material is constantly provided with change.  Genetic changes are critical for the propagation of species; the genetic material of a species must be variable in order for the species to adapt to the changes in the environment.  The frequency of mutations that occur in a species could be a key factor that determines the rate in which the species is adapting and therefore evolving(Stebbins and Ayala).  A species that contains the same genetic material for many generations will most likely become extinct, since its gene variants may no longer be favored by the new environmental conditions.  

One of the leading evolutionary biologist of the 20^th century, G.L. Stebbins ,along with professor Francisco J. Ayala of the University of California wrote: “Genetic changes underlie the evolution of organisms; mutations are the ultimate source of the genetic variation that makes possible the evolutionary process” (page 967).

Mutations that occur on genes create new forms called alleles. These new forms are passed down through generations.  The inheritance of the new alleles can benefit survival of the species but other alleles can carry detrimental effects.  For example, research showed that 46,880 years ago dogs carried a mutation for black coat color and recently, scientist have found that wolves that live in forested areas have inherited the allele (Anderson et al.).  Acquiring this melanistic allele benefited wolves who hunt in dark forests.  Dr. Anderson from Stanford University addresses the benefit of melanism in wolves.  “The potential selective value of dark versus light coat color has been suggested to include concealment during predation and/or indirect effects due to pleiotropy, but remains unresolved because the underlying gene(s) have not been identified”.  The inheritance of black coat allele has propagated quickly in wolf populations across North America.  Natural selection has increased the frequency of the allele but still the value of this adaptation is not understood (Anderson et al.).

The environment provides the pressure on the genetic material (the DNA), and during cellular division, mistakes happen in DNA replication (mutations).  These mutations can be passed on to the next generation (inheritance).  While some of them are harmful, others can provide advantage and increase survival and reproduction of the species (selection).  Natural selection works on mutations that already exist in the population.  Evolution occurs when mutations are selected and passed on through generations.

Work Cited

Ande

Anderson, T. M., et al. "Molecular and Evolutionary History of Melanism in North American Gray Wolves." Science 323.5919 (2009): 1339-43.

Pidwirny, M. (2006). "Concept of Ecological Niche". Fundamentals of Physical Geography, 2nd Edition. Date Viewed. http://www.physicalgeography.net/fundamentals/9g.html

Stebbins, G. L., and F. J. Ayala. "Is a New Evolutionary Synthesis Necessary?" Science 213.4511 (1981): 967-71.

Visser, M. E., L. J.M. Holleman, and S. P. Caro. "Temperature Has a Causal Effect on Avian Timing of Reproduction." Proceedings of the Royal Society B: Biological Sciences 276.1665 (2009): 2323-331. Print

What do I know the effects of Mutations

Mutations can occur in non-reproductive cells which are not inherited or can occur in reproductive cells which are inherited by the offspring.

Inherited mutations can have no effects on the phenotype if the mutation occurs in a non-coding region of a DNA segment or if the mutation occurs in a coding region but the mutation is synonymous. Some changes in the phenotype of the organism can occur if there is a change in amino acid. The protein will code for a different thing and cause the organism to have a defect or even cause death.

Mutations that occur in control genes can have negative or positive effects. Control genes regulate the expression of other genes. For example, the HOX gene is one that it is found in animals and it controls how the units (head, thorax, abdomen) of the animals body will be built. If a mutation occurs in one of these control genes the animal can be born with a defect in its body figure.

There are different types of mutations: Point mutations are the ones in which one DNA base is substituted with a different base. Frame shift mutations are either insertions or deletions of more than one DNA base. Inversion's, when an entire DNA segment is reversed. Chromosomal mutations where whole genes can be changed.

Final Draft Essay 2

Types of mutations and their inheritance: Somatic and Germ line

In genetics, a gene mutation is known as a change in the DNA sequence.   A mutation can be of small or large proportions, and cause a gene to lose its function and therefore prevent the organism from working correctly (Mutations involve). It can change only a single DNA base, or a big piece of DNA sequence in a chromosome (Mutations involve).  Some mutations can be silent, having no effect on the organism’s phenotype but other s can cause great changes in the organism’s physical traits (When genes go bad). There are two ways in which gene mutations occur: it can be inherited or can develop throughout lifetime.  While somatic mutations are not inherited, are caused by mutations in the individual cells and have no effect on the overall organism’s phenotype, germ line mutations are inherited, every cell has the mutation, and has effects on the phenotype; it is evident that these two types of mutations play a key role in evolution.

Somatic mutations affect somatic cells: regular cells that make up tissues of the body.  Somatic mutations occur while a cell is undergoing regular cell division, or mitosis (Inheritance pattern).  They can be found by comparing DNA from different cells from the same individual. These mutations occur after fertilization and throughout life; therefore they cannot be inherited. There are two general categories of mutations: point and chromosomal mutations (Types and causes). Point mutations are ones that change one nucleotide either by a deletion or substitution of a nucleotide in the DNA sequence (Types and causes). Chromosomal mutations change the DNA sequence with insertions, inversions or translocations of more than nucleotide (Types and causes). Usually somatic mutations are caused by point mutations and changes can go unnoticed or silent having no effect on the phenotype.  For example, if the mutation is cancerous then the body will keep producing these cells until the person dies.  Somatic mutations can cause damages in the bladder, liver and kidney function.  Among somatic mutations the most dangerous are the ones that occur in the regulation of growth and cellular division.  Cells start reproducing without control and start forming cancerous cells (Somatic mutations).

Germ cells or sexual reproductive cells are developed either into a sperm or an egg. The process of creating reproductive cells is known as meiosis and it is in this process that germ line mutations occur (Inheritance patterns). If a germ line mutation occurs all the germ cells in the body will contain this mutation.  Most dangerous germ line mutations are the ones that interfere with the function of the organism.  Such mutations may change the way we interact with diseases, or the environment. For example, red-greed blindness (Daltonism) affects your ability to distinguish colors (When genes go bad), and type 1 diabetes is a mutation that prevents you from producing insulin and digesting sugar (Type 1 Diabetes). However, there are germ line mutations that increase your chances of getting cancer.  If an individual carries such mutation in all its cells, fewer somatic mutations are needed to change it to the cancerous state.  For example, BRCA1 mutation is known to greatly increase the chances of breast cancer (BRCA1 and BRCA2).  This explains why cancers tend to run in certain families but not in others.

Not all the mutations are the same: they are different by type, effect, mechanism, and location.  Fortunately, there is repair mechanism: cells can fix mutations, otherwise there would be too many of them.  However, not all mutations are harmful.  Some of germ line mutations are neutral, or can actually improve your body.  These mutations are rare, but they happen often enough to contribute to the variation between individuals, or serve as material for evolution of the species.  The evolutionary roles of these two types of mutations are critical but different. Evolution of development tries to control all somatic cells from deviating from the original pattern from the first embryonic cell. Therefore, the evolutionary forces are keeping somatic cells similar. On the other hand, while most of the germ line mutations are disadvantageous for the development of the organisms, there are precious few that provide positive traits that can benefit the individual and promote evolution.

Works Cited

"BRCA1 and BRCA2: Cancer Risk and Genetic Testi - National Cancer Institute." Comprehensive Cancer Information - National Cancer Institute. Web. 04 Oct. 2011. <http://www.cancer.gov/cancertopics/factsheet/Risk/BRCA>.

"Germline Mutation Definition - Medical Dictionary Definitions of Popular Medical Terms Easily Defined on MedTerms." Web. 04 Oct. 2011. <http://www.medterms.com/script/main/art.asp?articlekey=15923>.

"Inheritance Patterns of Recessive and Dominant Mutations Differ - Molecular Cell Biology - NCBI Bookshelf." U.S National Library of Medicine National Institutes of Health. Web. 04 Oct. 2011. <http://www.ncbi.nlm.nih.gov/books/NBK21578/>.

"Mutations Involve Large or Small DNA Alterations - Molecular Cell Biology - NCBI Bookshelf." U.S National Library of Medicine National Institutes of Health. Web. 04 Oct. 2011. <http://www.ncbi.nlm.nih.gov/books/NBK21578/>.

"Mutations: Types and Causes - Molecular Cell Biology - NCBI Bookshelf." U.S National Library of Medicine National Institutes of Health. Web. 04 Oct. 2011. <http://www.ncbi.nlm.nih.gov/books/NBK21578/figure/A1886/?report=objectonly>

"Somatic Mutation - Cell Mutation." Cancer Prevention and Getting Through Treatments for the Different Types. Web. 04 Oct. 2011. <http://www.your-cancer-prevention-guide.com/somatic-mutation.html>.

"Type 1 - American Diabetes Association." American Diabetes Association Home Page - American Diabetes Association. Web. 04 Oct. 2011. <http://www.diabetes.org/diabetes-basics/type-1/>.

"When Genes Go Bad: Mutations and Disease." Understanding Genetics: Human Health and the Genome. Web. 04 Oct. 2011. <http://www.thetech.org/genetics/art04_bad.php>

Draft 1 Essay2: Somatic and germ line mutations

Somatic and germ line mutations

Draft 1

In genetics, a gene mutation is known as a change in the DNA sequence.  A mutation can be of small or large proportions, and cause a gene to lose its function and therefore prevent the organism from working correctly. It can change only a single DNA base, or a big piece of DNA sequence in a chromosome.  Some mutations can be silent, having no effect on the organism’s phenotype but other s can cause great changes in the organism’s physical traits. There are two ways in which gene mutations occur: they can be inherited or can develop throughout lifetime.  While somatic mutations are not inherited, are caused by mutations in the individual cells and have no effect on the overall organism’s phenotype, germ line mutations are inherited, and have effects on the phenotype; it is evident that these two types of mutations play a key role in evolution.

Somatic mutations affect somatic cells: regular cells that make up tissues of the body. Somatic mutations occur while a cell is undergoing regular cell division, or mitosis.  They can be found by comparing DNA from different cells from the same individual. These mutations occur after fertilization and throughout life, therefore they cannot be inherited. There are two general categories of mutations: point and chromosomal mutations. Point mutations are ones that change one nucleotide either by a deletion or substitution of a nucleotide in the DNA sequence. Chromosomal mutations change the DNA sequence with insertions, inversions or translocations of more than nucleotide. The most common mutations that occur in somatic cells are point mutations. Somatic mutations can have no effect on the phenotype, but more often affects the genotype.  Some of these changes can go unnoticed or silent.  If the mutation is cancerous then the body will keep producing these cells until the person dies.  Somatic mutations can cause damages in the bladder, liver and kidney function.  Among somatic mutations the most dangerous are the ones that occur in the regulation of growth and cellular division.  Cells start reproducing without control and start forming cancerous cells.

Germ cells or sexual reproductive cells are developed either into a sperm or an egg.  The process of creating reproductive cells is known as meiosis and it is in this process that germ line mutations occur. If a germ line mutation occurs all the germ cells in the body will contain this mutation. If a parent has a mutation in their germ cells its offspring will inherit these cells and carry the mutation.  Germ line mutations have a higher incidence of occurring in male gametes since males carry more sperm that are constantly produced through meiosis, compared to the fixed amount of eggs women carry.  To be able to find a germ line mutation, germ cells from two different individuals must be compared.  Germ line mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer.  Some examples are: Down syndrome, Cri du chat syndrome (cry of the cat), Turner Syndrome and breast cancer. Most dangerous germ line mutations are the ones that interfere with the function of the organism.  Such mutations may change the way we interact with diseases’, or the environment. For example, red-greed blindness (Daltonism) affects your ability to distinguish colors, and type 1 diabetes is a mutation that prevents you from producing insulin and digesting sugar. However, there are germ line mutations that increase your chances of getting cancer.  If an individual carries such mutation in all its cells, fewer somatic mutations are needed to change it to the cancerous state.  For example, BRCA1 mutation is known to increase the chances of breast cancer hundreds of times.  This explains why cancers tend to run in certain families but not in others.

Not all the mutations are the same: they are different by type, effect, mechanism, and location.  Fortunately, there is repair mechanism: or cells can fix mutations, otherwise there would be too many of them.  However, not all mutations are harmful.  Some of germ line mutations are neutral, or can actually improve your body.  These mutations are rare, but they happen often enough to contribute to the variation between individuals, or serve as material for evolution of the species.  

What do I need to find out about germ line and somatic mutations? What did my research tell me?

1.What are the type of mutations between germline and somatic mutations?

a. The mutations that occur in the germ line and somatic cells can be of the same type.

Some mutations that change a single nucleotide are called point mutations. These type of mutations cause deletion or substitution of nucleotide. Chromosomal mutations are mutations that cause insertions, inversions or translocations of more than one nucleotide.

 2. What are the different effects between germ line and somatic mutations?

a.The most important difference between germ line and somatic mutations is that germ line mutations are inherited through the germ cells or gametes, while somatic mutations occur during life in somatic or regular cells, and therefore cannot not be inherited by the following generation.

b.Germ line mutations are shared by all the cells of the same organism. To be able to find them it must be compared to a different individual. While somatic cells can be found by comparing DNA from different cells from the same individual.

3. Effects

a. Germ line mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer. Some examples are: Down Syndrome, Cri du chat syndrome (cry of the cat), Turner Syndrome and breast cancer.

b. Somatic mutations can have no effect on the phenotype, usually causes changes in the genotype. Some of these changes can go unnoticed or silent. If the the mutation is cancerous then the body will keep producing these cells until the person dies. Somatic mutations can affect damages in the bladder, liver and kidney function.

c. The effects of these mutations are different. Most dangerous germ line mutations are the ones that  interfere with the function of the organism.  Such mutations may change the we interact with diseases, or the environment. For example, sickle cell anemia,is a mutation that causes a change in shape of the red blood cell from concave to sickle form. Another example is  red-green blindness (Daltonism) affects your ability to distinguish colors, and Type 1 diabetes is a mutation that prevents you from producing insulin and digesting sugar.

Among somatic mutations the most dangerous are the ones that occur in the regulation of growth and cellular division. Cells start reproducing without control and start forming cancerous cells.

http://www.ncbi.nlm.nih.gov/books/NBK21578/ 

http://www.ncbi.nlm.nih.gov/books/NBK21578/figure/A1886/?report=objectonly 

http://www.medterms.com/script/main/art.asp?articlekey=15923 

http://www.thetech.org/genetics/art04_bad.php 

http://www.your-cancer-prevention-guide.com/kinds-of-cancer.html 

What do I know about somatic and germ line mutations?

1. The most important difference between germ line and somatic mutations is that germ line mutations are inherited while somatic mutations occur during life and are not inherited.

2.  Germ line mutations occur during the process of cell division known as meiosis. The cells produced in this process are the ones that will become either an egg or a sperm.

3. Somatic mutations occur while a cell is undergoing mitosis. The cells produced in this process will form part of organ tissue. Somatic mutations also occur after conception and during life.
 

Mitosis                Meiosis

  

4.  Germline mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer. Some examples are: Down Syndrome, Cri du chat syondrome (cry of cat), Turner Syndrome and breast cancer.

5.  Somatic mutations can have no effect on the phenotype, usually causes changes in the genotype. Some of these changes can go unnoticed or silent. If the the mutation is cancerous then the body will keep producing these cells until the person dies. Somatic mutations can affect damages in the bladder, liver and kidney function.

http://www.nature.com/scitable/topicpage/genetic-mutation-441

What is Genomics

Final Draft

What is Genomics?

      Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism.  A comprehensive study of a genome would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics (Brown, 2006).  This essay presents a short review of the three steps for a complete genome analysis.

The study of a genome begins with an examination of the sequence, or structural analysis.  A structural analysis refers to determining the sequence and location of each genetic element on a given DNA sequence. This is done by molecular and computing techniques including sequencing and assembly respectively.  Today, there are several sequencing techniques used for the study of genomes, but the first technique applied was the Sanger method (Sanger and Coulson, 1975).  Sanger sequencing method is based on a chain termination reaction that involves synthesis of DNA strands complementary to a single- stranded DNA template. The end product of this process is a library of short DNA fragments. To reconstruct the whole genome, these fragments have to be arranged together to form a long continuous sequence, in a process called sequence assembly (Myers et al., 2000).   
The ultimate goal of structural genomics is to identify every gene in the genome assembly.  Sequence inspection can be used to locate genes because they are not random series of nucleotides (structural units of DNA), but can be recognized for their distinctive features.  Since genes code for proteins, these features are well known.  For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met) found at the beginning of each protein (Brown, 2006).
The issue of finding genes is actually more complicated, because they are not continuous, and are often interrupted by the non-coding sequences called introns. Fortunately, these elements can also be identified, because they share common features between genes.  Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene.  The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structural analysis of the genome has been completed.  

As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this, it is easier to find the functions of the genes; this part is known as functional genomics.  As the genes regularly have many different functions, this task is often difficult.  
There are several approaches to determine the function of a gene.  For example, a common procedure is gene silencing, a method that uses mutations that change the original function of the gene and observe what happens to the organism (McManus and Sharp, 2002). The result of gene silencing is termination of gene expression which provides insights into the function.  Another way to determine gene function is to study the differences caused by the distinct alleles (an alternate form of a gene) of the same gene.  Usually, there is a common allele, or wild type, encoded by a certain sequence of a gene.  Individuals with genetic mutations in a gene sequence are compared to the wild type to see if they cause changes in function.  In addition, the location of gene expression can also be relevant to the gene function.  By observing where the gene is expressed within the organism, its purpose can be determined.  Usually, this is done either by attaching fluorescent tags to the sequences and tracking them with a microscope (Chalfie et al., 1994), or by identifying the increase in the amounts of the relevant RNA or protein in tissues (VanGuilder et al., 2008).  For example, if the protein that the gene encodes is found in the brain, then its function has to do with the brain activity.  Finally, the data gathered from the approaches described above can be used to study genetic pathways, in other words, tracking interactions between different genes. The goal of functional genomics is to determine gene function, to know how all the genes in an organism work, and to establish all the characteristics it has.

The final approach of the comprehensive genome study is comparative genomics. This area focuses on comparisons of genomes between related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which describe how genomes acquired their structure.  It has been observed that different organisms often carry the same genes known as homologous.  Even distantly related organisms share common genes because of their common ancestry. Genes that are important change slowly because random changes can disturb their function, while genes that are not so critical change faster, and are found to be more different when compared between species (Oleksyk et al., 2010). This is an important point, because comparative analysis of genome sequences can point out the important genes maintained by selection. On the other hand, finding genes that are divergent between species can explain differences between them.  For example, comparisons between the human genome and that of the chimpanzee, shows genes that are involved in developing superior brain structure and allows humans to use speech (Enard et al., 2002; Fisher and Scharff, 2009).  In other words, comparative genomics can give a scientific answer to one of the most important questions: “what makes us human”?

In short, this essay has reviewed the three stages of the study of a genome.  Together they are combined in Genomics, a science that studies genomes, the entire DNA codes found in each of the chromosomes that a given organism carries.  A comprehensive genome study involves all three major parts: structural genomics, functional genomics and comparative genomics.  Structural genomics focuses in sequencing and assembly of the genome for gene location.  Functional genomics is the area that determines that function of the genes.  Finally, comparative genomics focuses on comparing genomes of related species to determine the differences and similarities found between them.

Works Cited

Brown T.A. (2006). Genomes 3. 3rd ed. Garland Science Publishers. Oxford.713p.

Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D (1994). "Green fluorescent protein as a marker for gene expression". Science 263 (5148): 802–5

Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Pääbo S (2002). "Molecular evolution of FOXP2, a gene involved in speech and language". Nature 418 (6900): 869–72.

Fisher SE, Scharff C (2009). "FOXP2 as a molecular window into speech and language". Trends Genet. 25 (4): 166–77

McManus, M.T. & Sharp, P.A. (2002) “Gene silencing in mammals by small interfering RNAs”. Nature reviews. Genetics 3, 737-47

Myers EW, Sutton GG, Delcher AL, et al. (2000). "A whole-genome assembly of Drosophila". Science 287 (5461): 2196–204

Oleksyk TK, Smith MW, O'Brien SJ (2010) “Genome-wide scans for footprints of natural selection”.  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 365(1537):185-205.

Sanger F, Coulson AR (1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase". J. Mol. Biol. 94 (3): 4418

VanGuilder H D, Vrana KE, Freeman WM (2008). "Twenty-five years of quantitative PCR for gene expression analysis". Biotechniques 44 (5): 619–626

What is Genomics?

 Draft 2

 What is Genomics?

                Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism. A comprehensive genome study would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics (Brown, 2006).  This essay presents a short review of steps for complete genome analysis.

The study of a genome begins with the first examination of the sequence, or structural analysis.  A structural analysis refers to determining the location of each gene on a given DNA sequence. This is done by molecular and computing techniques which include sequencing and assembly respectively.  Today, there are several sequencing techniques used for the study of genomes, but the first technique used was the Sanger method (Sanger and Coulson, 1975).  Sanger sequencing method is a chain termination reaction that involves synthesis of DNA strands that are complementary to a single- stranded DNA template. The end product of this process is a library of short segmented fragments of DNA. To reconstruct the whole genome, these fragments are then arranged together to form a long continuous sequence, in a process called sequence assembly (Myers et al., 2000).

The ultimate goal of structural genomics is to identify every gene in the assembly.  Sequence inspection can be used to locate genes because they are not random series of nucleotides (structural units of DNA and RNA), but can be recognized for their distinctive features.  Since genes code for proteins, these features are well known.  For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met) found at the beginning of each protein (Brown, 2006).

The issue of finding genes is actually more complicated, because they are not continuous, and are often interrupted by the non-coding sequences called introns. Fortunately, these elements can also be identified, because they share common features between the genes. Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene. The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structural analysis of the genome has been completed.

As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this, it is easier to find the functions of the genes; this part of the study  is known as functional genomics.  As the genes regularly have many different functions, this task is often difficult.  Functional genomics is also concerned with interactions between genes and functional differences between different variants of the same gene. There are several approaches to determine the function of a gene. For example, a common procedure is gene silencing which is a method that uses mutations that change the original function and observe whats happens to the organism (McManus and Sharp, 2002). The result of gene silencing is termination of gene expression. The result of gene silencing provides insights into the function Another way to determine gene function is to study the differences caused by distinct alleles (an alternate form of a gene) of the same gene.  Usually there is a common allele, or wild type, encoded by a certain sequence of a gene.  Individuals with genetic mutations in a gene sequence are compared to the wild type to see if they cause change in function. Sometimes the location of gene expression can be relevant to gene function.  Therefore, by observing where the genes is expressed in the organism its purpose can be determined.  This is usually done either by attaching fluorescent tags to the sequence and tracking it with the microscope (Chalfie et al., 1994), or identifying the increase of the RNA or protein in tissues (VanGuilder et al., 2008). For example, if the protein that gene encodes is found in the brain then its function has to do with brain activity. Finally, the data gathered from the approaches described above can be used to study  genetic pathways, in other words, tracking interactions between different genes. The goal of functional genomics is to determine gene function, to know how all the genes in an organism work, and to establish the characteristics it has.

The final approach of the comprehensive genome study is comparative genomics. This area focuses on comparisons of  genomes between related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which describes how  genomes acquired their structure.  Often, it has been observed that different organisms carry the same genes, they are known as homologous.  Even distantly related organisms share common genes because of their common ancestry. Genes that are important for organisms function change slowly because random changes can disturb their function, while genes that are not so critical change faster, and are found to be more different when compared between species (Oleksyk et al., 2010). The importance of this is that comparative analysis of genome sequences can point out the important genes, those that have been maintained by selection. On the other hand, finding genes that are different between species can help find differences between them. For example, comparisons between the human genome and  the chimpanzee genomes show genes that are involved in developing superior brain structure, and allows humans to have speech (Enard et al., 2002; Fisher and Scharff, 2009).  In other words, comparative genomics can give a scientific answer to one of the most important questions: “what makes us human”?

Genomics is a science that studies genomes, and a genome is the entire DNA code found in each of the chromosomes that a given organism carries. A comprehensive genome study involves three major parts which are structural genomics, functional genomics and comparative genomics. Structural genomics focuses in sequencing and assembly of the genome for gene location. Functional genomics is the area that determines that function of the genes.  Finally,  comparative genomics focuses on comparing genomes of related species to determine the differences and similarities found between them.

REFERENCES

Brown T.A. (2006). Genomes 3. 3rd ed. Garland Science Publishers. 713 p.
Sanger F, Coulson AR (1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase". J. Mol. Biol. 94 (3): 441–8
VanGuilder H D, Vrana KE, Freeman WM (2008). "Twenty-five years of quantitative PCR for gene expression analysis". Biotechniques 44 (5): 619–626
Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D (1994). "Green fluorescent protein as a marker for gene expression". Science 263 (5148): 802–5
Oleksyk TK, Smith MW, O'Brien SJ (2010) Genome-wide scans for footprints of natural selection.  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 365(1537):185-205.
Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Pääbo S (2002). "Molecular evolution of FOXP2, a gene involved in speech and language". Nature 418 (6900): 869–72.
Fisher SE, Scharff C (2009). "FOXP2 as a molecular window into speech and language". Trends Genet. 25 (4): 166–77
McManus, M.T. & Sharp, P.A. (2002) Gene silencing in mammals by small interfering RNAs. Nature reviews. Genetics 3, 737-47
Myers EW, Sutton GG, Delcher AL, et al. (2000). "A whole-genome assembly of Drosophila". Science 287 (5461): 2196–204

What is Genomics?

Draft 1

What is Genomics?

Thesis statement:  Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism. A comprehensive genome study would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics.

Topic Sentence 1: To begin the study of a genome, the first examination is structural analysis of the genome.  A structural analysis refers to the location of each gene on a given DNA sequence. Structural analysis is done by molecular and computing techniques which include sequencing and assembly respectively.  Today, there is several sequencing techniques used for the study of a genome. The first technique that was used is the Sanger method.  Sanger sequencing method is a chain termination reaction that involves the synthesis of DNA strands that are complementary to a single- stranded DNA template (1). The end product of sequencing by the Sanger method is short segmented fragments of DNA. To form the whole genome sequence, the DNA fragments are arranged back together, forming a long continuous sequence of DNA, in short terms, sequence assembly.   The ultimate goal of structural genomics is to identify every gene in the genome sequence.  Sequence inspection can be used to locate genes because genes are not random series of nucleotides (structural unit of DNA and RNA) but instead have distinctive features. For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met).

The issue is complicated, because genes are not continuous, and are interrupted by the non-coding sequences called introns. However, these elements can also be identified, because they have common features. Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene. The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structure of the genome has been completed.   

Topic Sentence 2: As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this it is easier to find the functions of the genes. Functional genomics is the part of genome study where the functions of genes are determined.  As the genes regularly have many different functions, this task is often difficult.  Functional genomics is also concerned with interactions between genes and functional differences between different variants of the same gene, as in cancer studies.
function
 Topic Sentence 3: Comparative genomics is the part of that compares genomes of related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which is how did genomes acquire their present characteristics.  And one of the most important questions it studies is “what makes us human”?