Epigenetic Analysis Sequencing Methods

Epigenetic Analysis Sequencing
Epigenetics represents a complex layer onside DNA sequence reflecting the environmental factors.
It studies the changes in organisms lead to gene expression level change but the genetic code stay
the same. Epigenetics factors play an important role in regulating gene expression. There are two
main components of the epigenetic code, DNA methylation and histone modification. Epigenetics
changes are common in different areas, across different species. For human, epigenetics is extremely
important on complex disease or disorder studies.
Compared with genetics sequencing, most epigenetics applications are suitable for using short–read
sequencing. It still requires 25–75bp in length to confidently map a DNA fragment to its correct
reference genome. Most of the epigenome methods require high resolution and some of them even
require base–pair resolution. High resolution is essential for determining the precise DNA sequence
bound by transcription factors and other regulatory elements. Besides that, the higher the solution,
the easier to identify single binding sites within a cluster of closely spaced sites. The resolution of
the epigenome is important to understand chromatin structure. There are various epigenomic
methods that have been described in the previous paper. So my project is about different high–
resolution methods to study diverse aspects of the epigenome. Especially I focus on ChIP–seq
(Chromatin Immunoprecipitation sequencing) technique's analysis and its application direction, as
an example to represent the way to use big data in epigenetics. ... Show more content on
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They summarized how various genome–wide tools allow studying the diverse aspects of the
epigenome from five different aspects. I am going to focus on three parts of
... Get more on HelpWriting.net ...

Sequencing Program Analysis
Sequencing Programs: An Introduction to Phred, Phrap, and Consed DNA is life, and life is
abundant on planet Earth. The barren surface crawls with untold trillions of unique genetic codes,
turning the land rich and green. The ocean bursts species with DNA that enables a cold and watery
existence. Then there is the life unseen, hidden for four billion years from the naked eye. All
diversity is life, and all of life is DNA. At its heart, the goal of science is organizing observations
and quantitative data which define the biological processes and relationships of species; however,
the field of genetics is uniquely complicated in this pursuit due to an infinite source of DNA subjects
to study and an ever shifting genetic landscape which refuses ... Show more content on
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The primary purpose of Consed is to provide scientists a program to view Phrap data, and is in
essence an auto–finishing tool. Data can be viewed in a variety of ways, including graphical, and
can generate various reports. Additionally, the program can suggest useful possibilities at specific
sequence sites, such as primers for amplification, or to provide an overview, which will allow the
user to focus on areas of the sequence with low quality scores. The editing process allows the user to
manually correct the final product. Although manual editing is allowed, the purpose of automation
with Consed remains its primary feature of attraction, which helps remove the bottleneck of
sequencing data waiting to be finished, and thus drives higher productivity (Gordon, Desmarais, &
Green,

Gene Sequencing : Genes And Genes
"That which we call a rose by any other name would smell as sweet" (Shakespeare, 55), and the
reason why is found in the rose's genome. "Simply put, it [a genome] is the order in which the letters
of the genetic alphabet are arranged along the chromosomal DNA strands. . . ." (Richards and
Hawley, 279). Genomes are responsible for the structure, organization, and mechanics of organisms.
Due to the precedence DNA has over life, scientists have, for decades, worked to uncover the
mysteries found within our genomes. The process of organizing and identifying different genes is
referred to as Genome (or Gene) Sequencing. Gene Sequencing involves two aspects: gene location
and gene function. Genes that are frequently inherited together are ... Show more content on
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The fragments created are unique to that section of DNA, and can be used to identify that specific
piece of DNA. Scientists use this method to map both human and animal genomes. The information
gathered from these maps is compiled in the international GenBank. Scientists also study gene
function. This is more complicated than finding gene location due to the fact that genes influence
each other through epistasis and polygenic inheritance. Scientist can use genes with known
functions to make educated guesses about the function of unknown genes based on similar structures
within the gene. Mutations, and the effects they have, also helps scientists to understand gene
function. By locating which gene has been mutated and observing the result of that mutation,
scientists can determine that gene's function. The Human Genome Project (HGP) was founded in
order to sequence and identify the entire human genome, and to develop databases of genetic and
physical maps of different sequences. It later expanded to include other countries and became
known as the International Human Genome Sequencing Consortium. Their efforts correlated with
the research done by a biotechnology company called Celera Genomics, Inc. Based on both of their
results, the human genome contains approximately 35,709 different genes (Richards and Hawley,
299, 303). Interestingly enough, the results showed that every

Sequencing Is The Most Widely Used Targeted Sequencing Method
Exome sequencing is the most widely used targeted sequencing method. The exome only represents
less than 2% of the genetic code, but contains about 85% of known disease–related variants, making
a cost–effective alternative to whole–genome sequencing2. Exome sequencing detects variants in
coding exons, with the capability to expand targeted content to include untranslated regions and
microRNA for a more comprehensive view of gene regulation3. DNA libraries can be prepared in
one day and require only 4–5 Gb of sequencing per exome4. Exome sequencing enables researchers
to focus their resources on the genes most likely to affect phenotype, it has a wide range of
applications, including population genetics, genetic disease, and cancer studies3.
Like other next–generation sequencing methods, three general steps are required for exome
sequencing: library creation, sequencing, and data analysis. The size and quality of tested samples
are screened before establishing the library. In library creating, DNA molecules are fragmented into
a suitable size and fused with platform–specific adapters. After size selection step free adapters
elimination, PCR is performed to select for molecules containing adapters at both ends and to
generate sufficient quantities for sequencing2. The sequencing is performed in specific machine
such as Illumina Hi–Seq Platform, the working principles were discussed in detail in Topic Three,
however, in exome sequencing, only exomes are selected, amplified and

Dideoxy Nucleotide Synthesis
The Sanger Sequencing method has Dideoxy nucleotides which are similar to deoxy nucleotides, but
they have one key difference, they lack a hydroxyl group on the 3' carbon of the sugar ring. In the
regular nucleotide, the 3' hydroxyl group allows a new nucleotide to be added to an existing chain
(which is responsible for polymerization). The dideoxy nucleotide has been added to the chain, there
is no hydroxyl available and no further nucleotides can be added. The chain ends with the dideoxy
nucleotide, which is marked with a particular color of dye depending on the base (A, T, C or G)
which it carries. The DNA sample to be sequenced is combined with a primer, DNA polymerase,
and DNA nucleotides (dATP, dTTP, dGTP, and dCTP). The four dye–labeled, ... Show more content
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The mixture was heated to denature the template DNA, then cooled so that the primer can bind to
the single–stranded template. Once the primer has been bound, the temperature was raised again,
allowing DNA polymerase to synthesize new DNA starting from the primer. The DNA polymerase
will continue adding nucleotides to the chain until it add a dideoxy nucleotide instead of a normal
one. At that point, no further nucleotides can be added, so that the strand will end with the dideoxy
nucleotide. The process was repeated in a number of cycles. At the end of cycle, the dideoxy
nucleotide will be incorporated at every single position of the target DNA in at least one reaction.
That is, the tube will contain fragments of different lengths, ending at each of the nucleotide
positions in the original DNA. The ends of the fragments will be labeled with dyes that will be
indicating their final nucleotide. The fragments won't be labelled and a matter of chance whether a
dideoxy nucleotide gets incorporated in a particular polymerization reaction. Some of the newly
synthesized pieces of DNA will consist only of normal, unlabeled nucleotides, and will simply end
when the

Cancer Genomics And Genetics, Biot 640 Group 3
Cancer Genomics and Genetics BIOT 640 Group 3 Dr. Anthony Cristillo By Joana Oduro, Melissa
Oladokun, Sonia Ottou, Taylor Perry, Sulalith Rajapakse, Meredith Rutledge Table of contents
Introduction 3 NGS–based RNA sequencing (RNA–Seq) 4 Chromatin immunoprecipitation
sequencing (ChIP–Seq) 7 Paired tumor–normal (T/N) whole–genome sequencing (WGS) 8
References 10 Introduction The relatively recent completion of the Human Genome Project has
prompted a change in the approach of a lot of the current endeavors by broadening cancer research
away from a focus on single genes, such as BRCA1 and BRCA2, to that of the entire genome of the
individual.(Pasche & Absher, 2011). Tailoring therapy is a well–entrenched strategy employed when
it comes to tackling cancer given that each patient harbors a unique constellation of different
permutations that influence the probability, onset, and progression of their disease. The difference in
disease prognosis can be mild to severe and is largely driven by the subtle but unique differences in
genetic makeup of individuals. High–throughput tools have been developed to analyze nucleic acid
and generate data that could help improve diagnosis and treatment of cancers by identifying new
potential biomarkers for disease and also potential drug targets for the development of new
therapies. This paper explores some of the available technologies that are at the forefront of

Sanger Sequencing Essay
Sanger Sequencing was introduced in 1977 by Frederick Sanger and has been extensively used for
at least 35 years (10,11). Even now, it is still frequently used for small scale sequencing work. No
breakthrough of whole genome sequencing techniques was made until the launches of Roche 454
GS20 (12) and ABI SOLID (13) in the mid 2000. Soon after that, Ion Torrent (14), PacBio (15) and
Illumina (16) platforms have been introduced and quickly occupied the market of genomic
sequencing. Not until recently, the third generation sequencing, such as the nanopore (17), has been
commercialized and initially tested. A timeline of the development of DNA sequencing platforms
was described in Figure 1.
2.1 Illumina
Illumina sequencing platform launches later than the other competitors but quickly dominate the
next generation sequencing market. By using the Sequencing by Synthesis (SBS) technology,
millions of base pairs of the whole genome sequence could be finished in a couple of hours.
The NGS sequencing in Illumina instrument is divided into four major steps: Library preparation; ...
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Emulsion oil was injected into the DNA, enzyme, reagent mixture to form "water–in–oil" emulsion
droplet. Each droplet contains single DNA fragment with synthetic enzyme.Inside of each droplet,
single nucleotide sequence binds onto the surface of the beads, an emulsion based PCR (em–PCR) is
performed to amplify the single fragment to multiple copies on the bead surface. Then the DNA–
captured beads are placed onPicoTiterPlate. This PicoTiterPlate contains 1.6 million wells. Each
well is 75 picoliters in volume and 44 uM in diameter. Free nucleotides (TAGC) with luciferaseare
flown sequentially onto the picotiterplate. Single nucleotide complements to the template will
generate light signal, which will be captured by CCD

The Human Genome Sequencing Project And Was It Worth Doing?
What was the human genome sequencing project and was it worth doing?
The HGP was a 13–year long project started in 1990 with the objective of determining the entire
human euchromatic genome sequence. It was a public funded project and the goal was to complete
the project within 15 years. Since its inception, the project had been met with scepticism from
scientists and commoners alike. One significant doubt was whether the astounding expenditure of
the project would outweigh the potential benefits from it. However, the incredible success of the
HGP became apparent very soon after completion. Not only did it mark the beginning of a new era
in medicine, it also made significant development in the various techniques that can be used for
DNA sequencing. This publicly funded, $3 billion project began formally in 1990, under the co–
ordinated effort of the United States Department of Energy (DOE) and National Institutes of Health
(NIH). Although destined to be completed in 15 years, rapid technological development accelerated
the completion date to 2003.
The goals of this project could be bulleted under:
– to identify approximately 20,000 – 25,000 genes in the human DNA
– to determine the sequences of the 3 billion chemical base pairs of the human DNA
– to store the acquired information in databases
– to address the different ethical and legal issues arising out of the project.
It was the world's first international collaborative biological project which saw participation

A Short Note On A Polymerase Chain Reaction ( Pcr ) Essay
My longest ongoing project began in October 2014 under the guidance of Dr. Daniela Vergara, a
postdoctoral researcher of the CGRI. Dr. Vergara guided another undergraduate student and me to
troubleshoot a protocol for a Polymerase Chain Reaction (PCR). The objective of improving this
protocol was to analyze phylogenetic relationships between local samples by amplifying and
comparing a region of Tetrahydrocannabinol Acid (THCA) Synthase Gene. My colleague and I had
applied for the Undergraduate Research Opportunity Program Grant, which funded our research and
allowed us to ascertain a successful protocol for this PCR and sequence the amplified region of
THCA Synthase Gene. However, near the end of our project, we learned another university's
research team published nearly the same work we were performing, which encouraged us to further
our research before publishing. As new data became available, we observed eleven copies of the
THCA Synthase Gene, which provided our research with a new goal to develop novel primer sets
for each unique copy. My colleague and I each developed a novel set of primers and protocols
associated with those primers, which has allowed us to map the phylogeny through the variation of
these genes. Continuing to develop this research, we are analyzing possible correlations between the
variations of a certain paralogs in relation to the phenotype or physical traits of the plant. We plan to
publish the phylogenetic relationships we discovered, as well as

Benefits and Obstacles of Genetic Sequencing
"The Human Genome Project has already fueled the discovery of more than 1800 disease genes"
(Human, 2010). Genetic sequencing is a vastly expanding industry that began with the Human
Genome Project in the 1990s. The Human Genome Project was an ambitious endeavor that
undertook the challenge of sequencing the entire human genome which is composed of billions of
base pairs. Although this was no easy challenge, the project proved successful and in 2003
researchers finally sequenced a complete set of human Deoxyribonucleic Acid (DNA). This
achievement was the beginning of a new era. The success of the Human Genome Project has
enabled scientist to sequence an individual's entire genome; this capability has presented both
benefits and obstacles. Personalized genomic sequencing is already beginning to prove valuable in
not only the medical field but is also being integrated into other fields such as criminal justice.
However, genomic sequencing has generated controversy because of the questions about privacy,
costs, ethics, and dependability. Genetic sequencing is a vastly expanding field that has economic,
political, and social benefits, but the American Medical Association needs to adopt policies to
resolve ethical uncertainties pertaining to the practice.
The essence behind genomic sequencing is deoxyribonucleic acid (DNA). Regardless of shape, size,
color, species, or even kingdom, almost every single organism has DNA. DNA is composed of four
different base pairs: adenine,

Sequencing Genes Of Supercentenarian Essay
Sequencing genes of Supercentenarians & Applying Personal Genetic Data to Injury Risk
Assessment in Athletes
Abstract
These two research lab articles from Professor Stuart Kim's at Stanford University show the value of
information that can be collected from sequencing genes of different individuals. while the first
article uses genetic research to provide valuable information that can help reduce sports injuries and
optimize nutrition, the second article explores the genetic basis of extreme human age.
Introduction
Genetic knowledge can be applied and give us lots of unique information about individuals.
although Environmental influences play a huge role in the outcomes of physical traits, a version of a
gene, in almost every case, can give us a particular outcome. Reseachers can use this to see if such
genetic knowlege can help determine human's longevitivity and also predict risk of sport inhury in
athletes. Previous studies show that Supercentenarians, the worlds older people, age 110 and above
have escaped lots of age–related Diseases. knowing this information, the team went on and collected
17 of world's oldest people and sequenced their genes. ( qoute) On the second article, the team
collected 14 athletes from the Stanford University Triathlon Team and studied their genotypes to get
information that could lead to individualized sport injuries and nutrition uptake.( qoute) ... Show
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unfortunatley , their result did not show any single gene that can explain such a big effect. thereore,
the team concluded that it must be a goup of genes or things that are interacting in more of complex
level to produce human

Genome Sequencing Of A Plant
Genome sequencing of a plant creates a genomic resource for the plant with the help of which
further studies can be conducted on it. But this kind of a comprehensive resource is only available
for a few species. The plants that are recently making their presence felt internationally lack this
kind of a resource despite having numerous health benefits. A valid collection of genome wide
screening markers can add to the genomic resource for such plants. One such crop is Stevia
rebaudiana, belonging to the genus Stevia of the sunflower family (Asteraceae), commonly known
as Stevia, Sweet Leaf, Sweet herb of Paraguay, Honey Leaf and Candy Leaf (Madan et al., 2010).
Although it is native to Paraguay, it is now successfully being cultivated throughout the world as an
important exotic crop. It is widely grown for its sweet leaves, the source of sweetener products
known to contain 4–15% of steviosides which are estimated to be 100–300 times sweeter than
sucrose (Mondaca et al. 2012; Ishima and Katayama, 1976; Tanaka, 1982; Raji Akintunde
Abdullateef and Mohamad Osman, 2012). Being a zero calorie sweetener it is finding wide market
as it is safer and healthier since calories can lead to obesity, a risk factor for some chronic diseases
such as diabetes mellitus, hypertension, cardiovascular diseases, etc(Savita, Sheela, Sunanda,
Shankar, & Ramakrishna, 2004). Research also shows its effect on decrease in fertility of male rats
(Melis 1999) and adult female rats of proven fertility

Dna Sequencing Essay
DNA Sequencing: Algorithms that Convert Physical to Digital
EFFECTS:
DNA sequencing, specifically with small "nanopore" sequencers, have the potential to advance
medicine by increasing scientific knowledge of diseases and improving medical diagnosis in remote
areas. The leading sequencer today is the MinION, which is an incredible 10x3x2cm and only
requires a USB connection to a computer [5]. The MinION currently can sequence viral and
bacterial genomes, but will expand to include full human genomes. The MinION's size and
capabilities allow it to target the microscopic source of ailments outside of the laboratory and in a
greatly reduced amount of time.
Soon after its deployment in 2014, the MinION was used to sequence a salmonella ... Show more
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A 100mV voltage is applied across the protein, which draws the DNA through the pore. When a
DNA nucleotide is in the pore, a sensor records the change in current as an event [1].
This change in current is stored in a FAST5 file type, which stores metadata and the events [7]. The
FAST5 data files then undergo "base calling"––correlating one of the four nucleotides in DNA with
each event––in Amazon Cloud with a software called Metrichor or with offline open–source
software called Nanocall [7]. To reduce error rates, base calling algorithms are based off the Viterbi
algorithm, which determines the most probable "path" based upon surrounding measurements. In the
case of base calling, the surrounding 5 or 6 nucleotides are examined, 5 having 1024 combinations
and 6 having 4096 combinations [9]. While using 6 nucleotides doubles the analysis time, it
improves the accuracy of base calling [5].
After base calling, the all analyzed events are compiled into a single complete sequence. This
sequence is then compared to sequences in databases such as What's in My Pot (WIMP) or 16S,
which match the sequenced DNA to a specific species [8]. Because of the high speed of the input
and base calling, usually species identification is done in real–time [8].
c. CONCERNS:
In the realm of DNA sequencing, two main security concerns could threaten the computer systems

Genotyping And Sequencing
Describe the difference between genotyping and whole genome sequencing in your own words. Be
specific in your answer.
Genotyping is basically whole genome sequencing done incompletely, it is looking at a small
specific portion of a chromosome instead of all of one's genes. Genotyping is used by companies
like 23 and Me, it is significantly cheaper than whole genome sequencing. Genotyping can gives
you the risk factors for some disease, however because it is incomplete it is fallible. The risk factors
for a disease are basically inferences and not even remotely factual. For example one person who
wanted to test companies like 23 and Me reported that many of the results were consistent with each
other, however in the case of prostate cancer one site stated that he was at ... Show more content on
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Genotyping does not just provide disease risks, it also can give one information about their ancestry.
Whole Genome sequence does not have the same variability because the entirety of an individual's
DNA is sequenced. Whole DNA sequencing however, is still not a crystal ball, it gives a much more
accurate reading of risk factors but for all but a small fraction of disease it cannot report anything
with absolute certainty. Whole genome sequencing used to cost billions of dollars to complete but
has drastically dropped in price, however it is still considered expensive. Whole Genome
Sequencing is often used as a diagnostic tool for many diseases. Many treatments are now starting to
be tailored to the specific patients. Genome sequencing is even being used on cancer cells.
Abnormalities in a person's DNA are used as a guideline to try to pinpoint what is causing a person's
disease, challenges arise when the disease that is discovered is unsolvable. There are many who are
against having both genotyping and

Sequencing The Unborn Summary
In the article, "Sequencing the Unborn", by Kai Kupferschmidt discusses a new procedure that could
change the way how genetic diseases are found in fetuses. Currently doctors are able to extract some
fluid in the womb or placenta, has a one percent probability that it could cause a miscarriage.
However a chemical pathologist, Dennis Lo discovered that there is enough of the fetuses DNA in
the mothers. Instead using the previous method mentioned, parents and doctors could instead use the
ten percent of fetus DNA that is in the mothers' blood. This can still be quite tricky, Lo stated when
knowing the parent's haplotypes, it is possible to figure out the fetuses genome. Jay Shendure, a
genome scientist has also found another method of doing so. In a study he conducted, they were able
to sequence a fetuses genome by using the mothers' plasma and father salvia. After giving birth, the
compared this to the genome found in the ... Show more content on Helpwriting.net ...
Any couple who's they themselves or their partner's family have a history of certain genetic diseases
or disabilities will feel pressured to have this testing done. This topic reminds of the movie Gattica,
where parents can now choose what traits their child will have, even removing conditions such
baldness and alcoholism. In one scene the parent have chosen to have this done with their second
born son, after conceiving their firstborn naturally. When they met with the doctors, the parent
express that they only want to insure that their child is healthy and leave the rest up to chance. But
the doctor they insist they don't, and they continue with the full procedure. I don't believe this could
happen if these testings advances. Today's culture is tries it's best to more accepting of one another,
if this continue I don't see future parents opting to do such testings. There will be some who do, but
again it will only be a small percentage of potential parents who will do

Using Dna Sequencing Analysis
Sarah Arraiga
English–7A
AotW Response #1
19 November 2017 In the article "Using DNA sequencing, study says dogs evolved from European
wolf" it states that some dogs back in the day were used as pets. In other places of the world they
were used for farming or for meat purposes. Some dogs were used as hunting helpers. Scientist
claim that dogs were tamed around the Ice Age in Europe. They say that many dogs have evolved
from the european wolf, which is now extinct. Scientists believe at first we stayed away from
wolves because they were big and mean. The wolves from today have nothing to do with dogs said
one scientist. In fact many scientists claim that tracing dogs' ancestors has been very hard because
many dog bones are similar to wolf

Pacbio Sequencing Report
The principle of PacBio sequencing is easily understood, which captures sequence information
during the replication process of the target DNA molecule. The template, called a SMRTbell, is a
closed, single–stranded circular DNA that is created by ligating hairpin adaptors to both ends of a
target double–stranded DNA (dsDNA) molecule [2]. When a sample of SMRTbell is loaded to a
chip called a SMRT cell, a SMRTbell diffuses into a sequencing unit called a zero–mode wave guide
(ZMW), which provides the smallest available volume for light detection [3]. In each ZMW, a single
DNA polymerase is immobilized at the bottom, which can bind to either hairpin adaptor of the
SMRTbell and start the replication. Four fluorescent labeled nucleotides, which generate distinct
emission spectrums, are added to the SMRT cell. As a ... Show more content on Helpwriting.net ...
If the lifetime of the polymerase is long enough, both strands can be sequenced multiple times
(called ''passes") in a single polymerase read. Moreover, the polymerase read could be split to
multiple reads (called subreads) by recognizing and cutting out the adaptor sequences. The
consensus sequence of multiple subreads in a single ZMW yields a circular consensus sequence
(CCS) read with higher accuracy. If a target DNA is too long to be sequenced only one time in a
polymerase read a CCS read cannot be generated, and only a single subread is output instead.
Whereas, the CCS sequences are usually generated by transcript sequencing due to its relatively
short length. According, Pacific Biosciences developed an independently protocol, Iso–Seq, for
long–read transcriptome sequencing, including library construction, size selection, sequencing data
collection, and data processing. Iso–Seq allows direct sequencing of transcripts up to 10 kb without
use of a reference

Ethical Issues Of Dna Sequencing
DNA sequencing is the act of identifying the exact order of nucleotides within a DNA molecule.
DNA sequencing did not begin until the 1970s–sanger sequencing method was developed. DNA
sequencing has allowed scientists to make advances in the biological and medical fields. While
DNA sequencing has contributed to major advancements in the medical field, it has also raised
ethical questions so those advances should be used on humans. DNA sequencing has allowed for the
human genome project to be completed under budget as well as ahead of schedule. The goal of the
human genome project was to sequence the entire human genome. To understand the importance of
DNA sequencing, an understanding of biology must first be in place. DNA is short for
deoxyribonucleic acid and can be found in all organisms. ... Show more content on Helpwriting.net
...
When the DNA of an organism undergoes a minor change, it can have massive effects on the
function and look of the organism. In the study of biology all organisms are theorised to have
evolved from a few cells that were alive during the creation of the earth. DNA is similar between all
organisms; an example would be how humans and bananas share 50% of the same DNA. DNA is
made up of adenine(A), Guanine(G), Cytosine(C), and thymine(T). These are called nitrogenous
bases. A nitrogenous base is made up of an organic molecule and a nitrogen atom. Adenine,
Guanine, Cytosine and thymine use hydrogen bond to form a base pair. Each nitrogenous base has a
specified bonding partner that it can only bond with. Adenine only pairs with thymine. Guanine only
pairs with Cytosine. There is another nitrogenous base called Uracil(U). However, Uracil is only
found in RNA and Uracil only replaces thymine. Each base is also bonded

Lesson 1 Sequencing Lesson
Lesson 1 will start off with a brief vocabulary lesson for the students that builds on cardinal
vocabulary words previously taught in math class (1, 2, 3, 4). This brief vocabulary lesson will help
students link these vocabulary words to sequencing events by teaching them the corresponding
ordinal number words (first, second, third, fourth). Students will have the opportunity to
demonstrate their understanding of sequential language and their ability recall a sequence of events
from a story in order in a meaningful way through the use of The Very Hungry Caterpillar by Eric
Carle. Students will have the chance to independently exercise the skill of sequencing when they are
asked to recall the events that take place in the story in the order that they happened in the story.
Students will show their ability to recall the events of the story and their ability to sequence ... Show
This lesson will help students to understand signal words (first, next, last) which are commonly
associated with sequencing in text. Once the students have been introduced to this language, they
will have a chance to practice sequencing events through the use of signal words to help
comprehend a text. I will read There Was an Old Lady Who Swallowed a Fly to the students. The
students will have to recall the different things that the old lady ate, in order, using signal words.
After the story, the students will have to draw three things the old lady swallowed in the correct
order. This activity allows the students to practice using the essential literacy strategy of sequencing
events to fully comprehend the text by having them to recall key details of the story, their
understanding of the syntax of signal words, and by drawing the events they were able to recall from
the

Next Generation Sequencing Is The Method Of Determining...
NEXT GENERATION SEQUENCING
Introduction
DNA sequencing is the method of determining the order of nucleotides in DNA. It includes the
method that is used to determine the order of four bases –adenine, thymine, guanine and cytosine in
DNA. DNA sequencing has greatly accelerated research and discovery in biological and medical
field. The first DNA sequence was obtained using two–dimensional chromatography, in the early
1970s by academic researchers which was laborious. Now DNA sequencing has become easier and
faster after the development of fluorescence–based sequencing methods with a DNA sequencer.
Uses of DNA Sequencing:–
DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions
(clusters of genes), full chromosomes or entire genomes. Sequencing gives the order of individual
nucleotides which is present in molecules of DNA or RNA isolated from plants, animals, bacteria, or
any other source of genetic information. This information is useful in various fields of biology and
other sciences like medicine, forensics, etc.
Molecular biology– Sequencing is used in molecular biology to study genomes and the proteins they
encode. Information which is obtained using sequencing allows researchers to identify changes in
genes, associations with diseases and phenotypes, and to identify potential drug targets.
Evolutionary biology– DNA is an informative macromolecule in terms of transmission from one
generation to another generation. DNA sequencing is

Essay On Genome Sequencing
Description Every state within the United States runs its own newborn screening program which test
for at least 30 serious conditions which are treatable if caught early. The program is designed to save
lives and uses the dried blood sample collected during the first week after birth. The blood sample is
used to measure the presence of disease markers. The current newborn screening programs are fast,
cost effective, and accurate in identifying disease before symptoms appear. Genome sequencing cost
have now decrease to a price range like other complex medical test to be readily available for
clinical application. It is possible for genome sequencing to replace or supplement the existing
traditional panels for newborn screening tests. The ... Show more content on Helpwriting.net ...
The participants will only be enrolled after participating in an informed consent process. The
participants have a choice on whether they want to receive the information or not. The focus of the
study is to determine how clinicians and families use the genomic sequence results in their decision
making. If a family wishes not to know their sequence information they do not have to participant.
The technological advances in DNA sequencing have made high throughout sequencing methods
faster and cheaper. In contrast this allows researchers to generate larger datasets to be used for
genome wide association studies to identify specific factors associated with human health and
disease. Specification The National Institutes of Health in 2008 implemented a genome wide
association studies policy to require the data from National Institutes of Health funded studies to
share collected data with the research community to maintain the Genotypes and Phenotypes
database. The participants privacy is protected through a controlled access policy with a requires
secondary use of data to be consist with the initial informed consent given. For future usage the
research must obtain another consent for the participants data to be used for future research expand
the database. For example, the HeLa Genome Data Use Agreement in August 2013 detailed the
importance of controlling data access to protect research participant privacy. The HeLa

The Human Genome and DNA Sequencing
A genome is the complete set of DNA, including all of its genes. Each genome contains all the
information needed to build that organism. In humans, more than 3 billion DNA base pairs are
present. For advance knowledge of molecular and evolutionary biology, it is crucial to sequence the
DNA of every human chromosome. This is quite huge in scale, as it sought to determine the order of
all 3 billion nucleotides in the human genome. Hence a number of sequencing techniques were
developed that at the same time emphasized speed without too much loss of accuracy.
DNA Sequencing
DNA sequencing was first devised in 1975 which came about because DNA sequence consists of
four different bases– A, T, C and G and the bases can be identified by DNA sequencing which
allows analysis of genes at the nucleotide level.
It can be applied in many areas of research including the polymerase chain reaction (PCR), a
method which rapidly produces many copies of DNA or a DNA fragment. Another important use of
DNA sequencing is identifying restriction sites in plasmids which are useful in cloning a foreign
gene into the plasmid. Prior to the development of DNA sequencing, molecular biologists had to
sequence proteins directly but now amino acid sequences can be determined more easily by
sequencing a piece of DNA and finding an open reading frame. Furthermore, a molecular biologist
can utilize sequencing to identify the site of a point mutation.
DNA Sequencing Basic methods
In the 1970s, the

Fat Body Sequencing Analysis
It is really interesting that the analysis of fat body sequencing has pointed to thems related to
nervous system plasticity in PFD group. In natural conditions the foraging onset is characterized by
a neuronal plasticity and anatomical changes in the mushroom bodies, which are essential for
learning connected to foraging (Coss et al., 1980; Brandon & Coss, 1982; Withers et al., 1993).
Recent studies showed a communication between hypothalamic neurons and adipose tissue in mice
through insulin and leptin, controlling the energy balance of fat and consequently hunger or satiety
(Dodd et al., 2015). Furthermore, a number of insects' octopaminergic neurons are involved in
nutritional signals transmission from peripheral organs, such as the fat body, to the brain (Roeder,
1999). Although the themes related to neuronal and synaptic plasticity have been found in the fat
body, this result may indicate a synergistic expression between this organ and the brain. This result
certainly needs a thorough study, but to our best knowledge it is the first time that the themes axon
... Show more content on Helpwriting.net ...
Alaux et al. (2011) also found similar results for Mvl, whose expression is connected to the sugar
responsiveness (Orgad et al., 1998) which is overexpressed in foragers brains (Ben–Shadar et al.,
2004). PFD group also showed high expression of the gene very low–density lipoprotein receptor–
like (XP_001122285). Provided that insects have no cholesterol, the mevalonate pathway is
metabolically diverted to the production of juvenile hormone (HJ) (Bellés et al., 2005). We can
speculate that in A. mellifera, XP_001122285 expression is associated with high titers of Juvenile
Hormone (JH) and can act as a carrier of this hormone receptor. If this speculation is correct, the
expression of such gene would also be associated with the forager status, where JH titles are higher
(Fluri et al.,

Essay On Human Genome Sequencing
1. Current challenges in human genome sequencing
Technologies in sequencing are highly accurate but have limitations in read–depth and read length.
Read–depth refers to sequencing the highly repetitive regions of DNA with few to no errors.
Illumina HiSeq and PacBio have allowed geneticists to fill in the gaps of the human genome saving
time and money. In the scope of the read depth issue, researchers are still having issues with
undetectable structural variants (SV) including copy number variants (CNV) and small nucleotide
polymorphisms (SNP). (Bickhart, et al. 2017).
Illumina HiSeq is one of the more accurate forms of DNA sequencing technology, about 99%
accurate. The newest version of HiSeq is TruSeq nano and NEBNext Ultra. Sequencing ... Show
New approaches to sequencing include Illumina, PacBio SMRT Chip technology and the nanopore
minION. Illumina is accurate about 99.9% of the time. PacBio is by far the most accurate of the
three sequencing technologies. Although the nanopore minION is not as accurate as PacBio SMRT
and Illumina, this technology is able to detect anomalies in the genome. All of these sequencing
technologies have a cost associated with them, but the Oxford Nanopore minION is the most
expensive.
Illumina is a less expensive way to sequence. At 99.9% accuracy, Illumina is able to provide short
read lengths to be analyzed using Phred. Phred is a base calling algorithm that calculates the
location of a fluorescent peak and records the base for that particular fluorescent label. This
technology is not ideal due to portability and sequencing prep. The DNA still has to be amplified to
create a cDNA library using bridge amplification. Illumina requires a polymerase and fluorescently
labeled dideoxynucleotide triphosphates (ddNTPs) followed by Sequencing by synthesis (SBS).
This is the final step in generating the wavelength reading of nucleotide bases. (White, et al. 2016)
The Oxford Nanopore minION sequencer is able to produce reads up to 300kb. Unlike Illumina and
PacBio, Nanopore technology can detect structural variants and cytosine modifications including
hydroxymethylcytosine, formylcytosine and methylcytosine. The purpose of this

Essay On Rna Sequencing
Introduction:
Humans have always been curious to find answers to various things of life. This curiosity and have
been a driving force for discovery. Over the years our tools have evolved from the basic light
microscope to high throughput DNA sequencers along with our understanding of the world around
us.
RNA sequencing is inspiring scientists to push the limits of current research methods in
understanding how the transcriptome shapes biology and much more. RNA sequencing is becoming
one of the most significant tools in the world of modern science.
RNA sequencing (RNA–Seq) is revolutionizing transcriptome studies. It's a highly reliable tool for
measuring gene expression across the transcriptome. Also, it's providing deep insight previously ...
Show more content on Helpwriting.net ...
This method doesn't require predesigned probes, the data sets have no bias(, allowing for
hypothesis–free experimental design2,3.
This type of NGS analysis is a powerful tool for transcript and variant discovery which otherwise
wouldn't possible using traditional microarray–based methods.
Wider Dynamic Range and Higher Sensitivity
Microarray measure continuous probe intensities. But RNA– Seq quantifies individual sequence
reads aligned to a reference sequence which produces discreet (digital) read counts2. Also, by
increasing or decreasing the number of sequencing reads (coverage level or coverage depth),
researchers can fine–tune the sensitivity of an experiment to accommodate different study
objectives. The digital nature of this process and the ability to control coverage levels supports an
extremely broad dynamic range, with absolute rather than relative expression values2–4.
Assuming 10–50 million mapped reads, the dynamic range of RNA–Seq spans 5 orders of
magnitude (>105) and is typically several orders of magnitude higher than most array technologies
(103)2,5. As a result, RNA–Seq has been shown to detect a higher percentage of differentially
expressed genes compared to expression arrays, especially genes with low abundance5,6.
Ability to Detect Alternative Splice Sites, Novel Isoforms, and Noncoding RNA
Beyond gene

Genealogy: The First Step In Sequencing My DNA
Analyzing a person's total DNA can tell you quite a bit of information about that person. In order to
acquire information about my genetic heritage, I would want my genome to be sequenced. From
here, I would want specific sections of my genome to be looked at, which would tell me information
about my ethnicity and relationships in regards to genealogy. Because such a small percentage of the
genome has been shown to code for genes that are functional, (approximately 3%) it would be this
portion of the genome that would be analyzed.1 The first step in sequencing my DNA would be to
send in a sample of my DNA via a buccal swab. The buccal swab collects the cells from the inside
of my cheek, and the sample is sent to a DNA testing lab.2 At the clinic, a DNA forensic scientist
might be one ... Show more content on Helpwriting.net ...
These sequences can code for different genes, and this information can tell me about different
mutations in my DNA that could have led to or could lead to potential medical problems, and the
sequence can also tell me things about my family's origins around the world, my ethnicity, and
potential genetic diseases that I could pass down to my children. Once my DNA has been sent to a
lab for analysis, a sequencing method can be used to tell me what my DNA sequence is. Because
there is the potential for the sample that I sent to not have a great deal of DNA available, polymerase
chain reaction may be used to amplify the DNA to get a better sample to analyze. In polymerase
chain reaction, they will take the small sample of DNA that I have provided along with two
oligonucleotide primers, Taq polymerase, and four deoxynucleotide triphosphate and amplify the
sample of DNA. In the first step, the DNA is heated to 95 degrees Celsius in order for the two
strands of DNA to separate from each other. After the solution has cooled down to 54 degrees
Celsius, short DNA primers hybridize to the DNA. Finally, after raising the temperature to 72
degrees

Sanger Sequencing Technique
High–throughput genome sequencing technologies are currently the important topic in the biology
and medicine that allow us to look at thousands of sequence reads at a time. High–throughput and
next generation sequencing technologies have largely been using for standard sequencing
applications. Anyway these new technologies bring with many new challenges for biologist and
bioinformatics people as how to process and interpret the massive amounts of biological data so as
to achieve at biologically significant results. We presented a concise description of most commonly
used sequencing technologies and the associated challenges below. Sanger sequencing: Sanger
sequencing method developed by Fred Sanger in 1977 and was the most extensively used

Sanger Sequencing: Polymerase Chain Analysis
Figure 1.1: A schematic representation of Sanger sequencing. The Sanger method uses
dideoxynucleotides that terminate newly synthesized DNA fragments at specific bases either A, T, C
or G. Then, the resulting fragments are resolved by electrophoresis through a denaturing
polyacrylamide gel in four parallel lanes, and the DNA sequence can be read (Rosenberg and
Pascual, 2014).
The initial Sanger sequencing method has been administered to several significant improvements
and developed remarkably over three decades. Even though cloning of DNA fragments into plasmid
vector was required in Sanger sequencing, the application of polymerase chain reaction (PCR)
(Saiki et al., 1988) for the amplification of specific DNA fragment in vitro has extensively

Persuasive Essay On Prenatal Sequencing
Prenatal Whole Genome Sequencing In recent years, fetal gene sequencing has been a controversial
topic of debate for various reasons. This sequencing gives parents their unborn child's full genetic
complex during pregnancy. Meaning, parents will know in advance the physical traits, any possible
disease development, or other complications. Patient care for future generations can be more
accurate and efficient with the use of the scanning. There are conflicts between parents on the
beliefs over this type of testing. Due to the immorality of obsessive parental influence, fetal
scanning should only be used for medical illness prediction. For centuries, the child's condition was
a mystery until birth, at which point most ailments could not be treated properly. Gender, physical
appearance, and well–being are the common traits that parents think about. However, Down
Syndrome, Phenylketonuria (PKU), and many other abnormalities are not typically taken into
consideration. Hope for a healthy child dominates preparation for possible future health
impairments. A parent does not wish to have an unhealthy child, therefore, in a form of rejection,
they do not financially prepare for such things. With the introduction of prenatal gene sequencing,
all of this ... Show more content on Helpwriting.net ...
Rather than saving up for future procedures to emend illnesses, parents could use their money for
plastic surgery. Physical appearance is a major factor in the representation of the family for most
mothers and fathers. These types of parents could go to the extent of making this their highest
priority among their children. Another reason for focusing fetal sequencing is an effect on parenting.
Revealing genetic disconformities could influence how parents discipline their future children.
Instead of providing proper discipline, parents would blame misbehavior on the genes rather than
intervene with guidance and

The Cannabis Genomic Research Initiative
Being engaged and intrigued by new information, the love for my coursework has grown every year;
however, the opportunity to discover novel information through my research is one of my most
intellectually stimulating experiences. Under the guidance of Dr. Nolan Kane, the Professional
Investigator of the Cannabis Genomic Research Initiative (CGRI), I have expanded my traditional
wet lab work to bioinformatics, hemp breeding, and leading a project I designed to analyze
differential RNA expression in Cannabis. Through my work and fascination with this four
nucleotide code, I create freedom in my research to learn about any other organism or genetic
disease that I hope to treat within my career.
My longest ongoing project began in October ... Show more content on Helpwriting.net ...
As new data became available, we observed numerous copies of the THC Synthase Gene, which
provided our research with a new goal to develop novel primer sets for each unique copy. My
colleague and I each developed a novel set of primers and protocols associated with those primers,
which has allowed us to determine the phylogeny and variation of these genes. Continuing to
develop this research, we are analyzing possible correlations between the variations of a certain
paralogs in relation to the phenotype or physical traits of the plant. We plan to publish the
phylogenetic relationships we discovered, as well as any possible correlation between genotype and
phenotype in October 2016. If a correlation can be concluded, these results and developed primers
would be the first marker–assisted breeding available to successfully determine the drug content of
Cannabis before flowering.
During testing our developed primers in August 2015, I began work on my Honor's Thesis to
understand mRNA expression changes during a common chemical treatment used by many growers
to change the sex of the plant for seed production. Through growing female plants and treating some
branches with silver thiosulfate, these plants will produce both male and female flowers, which can
be harvested throughout the growing process. These flowers will have RNA extracted at three time
points, which will then be processed, sequenced and

Sequencing Teaching Strategies
Sequencing
I will use the following teaching strategies to implement Sequencing within my classroom. I will
first start with creating a climate that engages all students. An example of this would be developing
a community of literacy learners utilizing classroom organization with everything being labeled, a
Word Wall, and by posting posters with words up within the classroom. Next, I would use Guided
Reading (known as the Heart of Instructional Reading) strategy before, during, and after to help my
students learn to read and read to learn. I learned about this particular teaching strategy within
Reading in Content 516.
Afterwards, I would teach students to examine ideas presented within the text through the use of
highlighting within

Genome Sequencing Essay
Cancer is first and foremost a genetic disease that is caused by mutations in somatic cells and
epigenetic aberrations in genes that control a range of cell processes(1). Genome sequencing of
many cancer patients has identified that over 500 human genes can lead to the development of a
cancer when mutations occur(2). Sequencing the genome of a single cancer patient can provide key
information about the tumour and type of genes involved in its development.
Genetic sequencing
Genome sequencing is determining the order of bases that make up a segment of a person's DNA.
The exome is the section of the genome that codes for proteins, approximately 1.5% of the human
genome(3). Exome sequencing was initially used to analyse the DNA or cancerous ... Show more
Sequencing the exome of the cancer patients' tumour would identify whether the growth, is
originally due to oncogenes or tumour suppressor genes and then the treatment can be tailored to
treat the specific needs of the patient.
Treatment
One of the most unusual things about breast cancer is that it has the potential to progress differently
in every patient, meaning every patient will react differently to any treatment provided (2). This
enforces the need for exome sequencing of the tumour to personalise the treatment given. One gene
that can play a role in the development of breast cancer is Human epidermal growth factor receptor
2 (HER–2)(7). If the HER–2 gene is present, then this gene codes for specific proteins which are
receptors on breast tissue cells. In a normal example the HER–2 receptors control cell proliferation
and apoptosis however, if this oncogene is activated HER–2 gene amplification takes place(8). This
leads to the over expression of HER–2 proteins causing HER–2 positive breast cancer, a specific
type of cancer with specific treatment(7).
One of the main targeted antibody treatments for breast cancer is trastuzumab. This works against
the HER2 positive breast cancers to inhibit the cells ability to receive the signals causing them to
grow(7). A diagnostic test is conducted to determine whether the target protein, HER2, is responsive
the

What Is Genetic Sequencing?
What is Genetic Sequencing? "If you could skip to the last chapter in your book of life would you
read it"? This is a common question asked to most people while they are growing up. Everyone
always viewed this question in a figurative sense and it made them ponder their future. However,
with genomic sequencing this question has become a real dilemma for doctors in the health
profession. Imagine that a sick baby enters into your office and you screen their genetic code for
kidney disease in the process of doing so you find that the child has a gene that will make him prone
to developing early–onset Alzheimer's disease. You walk towards the room and you have to make
the decision of what you are going to tell the parents. You can tell them of an incurable disease that
will take years to have an effect on their child or should you just let them worry about the issues
affecting their child now? This is one of the many ethical issues with genetic sequencing. Thesis
Genetic sequencing has been a ground breaking discovery in the medical field. This process allows a
doctor to take a patients DNA and determine what diseases that they are at risk for and what
preventative measures they take to help protect the patient from the disease. Some doctors use this
process as a last resort to diagnose younger patents when they don't know what is infecting their
patient. The problem that comes with this process is that normally doctors find something in the
genetic code that could be life

Helix High Sequencing Technology : Technology And Storage...
If 80 bucks and a spit are what it takes to access a human exome and expose genetic traits such
medical and dietetic predisposition, what would happen if we could on the same exon insert the
current and past medical record? For decades scientists have been searching for new and safer
means to store data. Yet, with the advance of technology, particularly, computer science generally,
this concern became a big dilemma for scientists because of the large amount of data produced daily
versus the gradual scarcity of secure storage warehouse for delicate data such as biological
hereditary information. As that concern for safe storage capacity grew much quicker than they
expected and the growth of the integration of computer science in the ... Show more content on
Helpwriting.net ...
In any case, however, this method offers great advantages. For instance, researchers have found it to
allow high density information to be stored in very small space. For instance, it is estimated that one
gram of single–strand DNS could store as one Exabyte of data (Church, Gao, & Kosuri, 2012).
Other scholars, such as Xiao, Lu, Qin, & Lai, (2006) reported that the use of DNA storage facilitates
the use of DNA as information carrier and the modern biological technology as the main
implementation tool that makes sequence hybridization and other techniques of isolation,
synthetization, amplification, digestion and sequencing of DNA very easy. Other researcher, such as,
Glenn (2011), indicated that this technology gave researchers like himself tools that are opening new
avenues of investigation and developing techniques, which offer answers to long–standing
ecological evolutionary curiosity.
Pitfalls and success of DNA as a mean of data storage
DNA as a mean of storage represents a large range of benefits to scientists and medical specialists,
which include, but not limited to storing early raw forms of data, like images and signals. However,
many researchers and groups, such as, Bradnam et al., (2013), Fritz, Leinonen, Cochrane, & Birney,
(2011),

Milestone Sequencing Essay
[57]. While some researchers [39], [56], have shown that drop out mostly occurs when students have
finished their coursework; during the years of study when learners are working on their dis–sertation
and when isolation is a common phenomenon. Others [58]–[60], have indicated that it is not the
stage at which the learner is at, but rather the lack of both academic and social integration (that is,
isolation itself) that affect doctoral learners' decision to either persist with their studies or not. In
Canadian universities, doctoral programs vary in structure and in the number of milestones doctoral
learners have to complete to earn their doctoral degrees depending on the institution and discipline
involved [61]. Generally, doctoral learners have to complete four common milestones. These
milestones include coursework, comprehensive exam, proposal, and dissertation. These milestones
can be completed by doctoral learners in both varying order and year of study based on their
doctoral discipline. In most cases, however, these milestones are completed in the order provided
above. Change of milestone completion sequencing is a department policy; as indicated by Ampaw
and ... Show more content on Helpwriting.net ...
The Four Supervisory Styles and Associated Supervisor Traits Based on Supervisory Management
Grid [50]. As far as doctoral learning is concerned, learner undertake a myriad of writing endeavors
[64] and the writing strategy they choose is consequential to the time they spend on it according to
Torrance et al. [51]. Torrance and his colleagues [51] used cluster analysis to identify three dif–
ferent student writing strategies, n = 101, based on the timing of their decision on the content of
their write–up. They grouped into three categories: planners, revisers, and mixed strategy writers.
See Table 1 1 for a brief description for each of the category. Table 1 1. Brief Description of Each of
the Graduate Students Writing Strategies Writing strategy Number Content of write–up decision

Essay On Whole Genome Sequencing
2.0 Materials and Methods
Whole genome sequencing (WGS) is one of the current methods used to obtain the entire genetic
composition of a particular patient. Once the sequence of DNA has been obtained the information
within the patient's genome is compared to a reference genome so that potentially pathogenic
mutations can be identified. Regions of DNA that are of interest are validated following the
procedure outlined below.
Primer design
Specific DNA loci were obtained from analysts in the form of Excel spreadsheets. These coordinates
were visualized using the genome browser build 19 on the UCSC website. The DNA sequence that
was taken was approximately 900 bp on either end of the region which was to be amplified. The
DNA sequence which ... Show more content on Helpwriting.net ...
This extension period was set for 7 minutes. 35 cycles were run when amplifying particular regions
of DNA obtained from probands and their respective families. Note primers were tested with
controls using the hotstart PCR conditions before primers were run with the patient's DNA.
Visualizing PCR product
Agarose gels were run to determine whether amplification of the targeted region of DNA was
successful. 1% gels were made using 50mL of 1X TAE buffer and 0.5g of agarose. 2.5mL of
Ecosafe dye was added to the gel before mixing and then cooling in a gel rig. 1.0mL of loading dye
was mixed with 4.0mL of DNA from PCR tubes. DNA samples were then loaded in their respective
wells along with 5mL of 1kb ladder to approximate band sizes during visualization of the gel. Gels
were visualized using UV light set at a wavelength of 302nm. Each gel was exposed to UV light for
10 seconds before the image was captured with an Azure gel imaging system.
Purification
PCR tubes were ready for purification when a single DNA band was present per lane on the agarose
gel. If multiple bands were obtained in a single lane the PCR process and gel visualization process
was repeated however, the denaturation temperature was run at a higher temperature to prevent non–
specific binding of the primers to the DNA template. The purification process used an Invitrogen
PCR clean–up kit. 5mL of charge switch beads

Dna Sequencing Synthesis
Biotechnology is field where everything constantly changes. The rapid growth and development of
cutting edge technology is invariably dependent on innovation of scientists and their ability to see a
potential in a basic molecular technique and apply it to new processes. DNA sequencing is also
dependent on our ability to use gel electrophoresis to separate strands of DNA that differ in size by
as little as one base pair.
Originally there were 2 methods which were invented around 1976, but only one is widely used: the
chain–termination method invented by Fred Sanger.
The other method is known as the Maxam–Gilbert chemical degradation method, which is the less
used method but is still used for specialized purposes, such as analyzing DNA–protein ... Show
Four different PCR reaction mixtures are prepared, each containing a certain percentage of
dideoxynucleoside triphosphate (ddNTP) analogs to one of the four nucleotides (ATP, CTP, GTP or
TTP).
Synthesis of the new DNA strand continues until one of these analogs is incorporated, at which time
the strand is prematurely truncated. Each PCR reaction will end up containing a mixture of different
lengths of DNA strands, all ending with the nucleotide that was dideoxy labeled for that reaction.
Gel electrophoresis is then used to separate the strands of the four reactions, in four separate lanes,
and determine the sequence of the original template based on what lengths of strands end with what
nucleotide.
In the automated Sanger reaction, primers are used that are labeled with four different coloured
fluorescent tags. PCR reactions, in the presence of the different dideoxy nucleotides, are performed
as described above. However, next, the four reaction mixtures are then combined and applied to a
single lane of a gel. The colour of each fragment is detected using a laser beam and the information
is collected by a computer which generates chromatograms showing peaks for each colour, from
which the template DNA sequence can be

Sanger Sequencing
Introduction:
DNA sequencing is a method for determining the precise order of nucleotides present in a given
DNA molecule [1]. The Sanger and Gilbert methods of sequencing DNA are referred to as first–
generation sequencing because they were the first to be developed. The Sanger sequencing, also
known as the chain terminating method, developed in 1975 by Edward Sanger, was considered the
gold standard for nucleic acid sequencing for two and a half decades (Sanger et al., 1977). The
Human Genome Project was accomplished with first–generation sequencing in 2003, known as
Sanger sequencing. The Human Genome Project (HGP) was an international cooperative venture
established to sequence the 3 billion base pair (~25,000 genes) in the human genome. ... Show more
The material of the substrate/wafer can be conventional silicon, glass, plastic, COC or any of a
variety of materials that can be structured. Exemplary techniques for introducing the patterning into
the substrate include photolithography, nanoimprint lithography, embossing of the structures into a
plastic/COC based material and injection molding of a plastic or COC into a master mold that has
the structures patterned into it. Photolithography based approaches will typically involve use of a
photoresist that is patterned with a stepper or mask aligner, exposed with radiation which transfers
the pattern present on a reticle/photomask into the photoresist, and then the resist is developed to
yield a structured film (photoresist) on top of the substrate. The structured resist is potentially the
final substrate which can be used for subsequent gel coating or the pattern in the resist can be
transferred into the substrate via follow on processing. The follow on process steps will typically
include reactive ion etching (plasma based etching) or a wet etch (chemically based) process. If the
pattern is transferred into the substrate, the patterned photoresist is subsequently removed to yield
the patterned substrate for subsequent gel coating. It may be desirable to use a sacrificial film of a
material such as Chrome or Titanium (a metal) under the photoresist, and first transfer the pattern in
the photoresist to the metal film and then use that film as a hard mask by which the pattern is
transferred into the substrate. Following pattern transfer into the substrate, the films are removed
and therefore considered sacrificial to the fabrication process. If nanoimprint lithography is used, the
imprinted photoresist can be a sacrificial material and similarly be used as an intermediate tool to
transfer the patterned resist into the

The Cannabis Genomic Research Initiative
Being engaged and intrigued by new information, my love for my coursework has grown every
year; however, the opportunity to discover novel information through my research is one of the most
intellectually stimulating experiences. Under the guidance of Dr. Nolan Kane, the Professional
Investigator of the Cannabis Genomic Research Initiative (CGRI), I have expanded from traditional
bench work to bioinformatics, hemp breeding, and leading and designing my own project analyzing
differential RNA expression in Cannabis. Through my work and fascination with this four
nucleotide code, I am providing freedom within my research to learn about any other organism or
genetic disease that I hope to treat within my career.
My longest ongoing project ... Show more content on Helpwriting.net ...
As new data became available, we observed numerous copies of the THC Synthase Gene, which
provided our research with a new goal to develop novel primer sets for each unique copy. My
colleague and I developed a novel set of primers and protocols associated with those primers, which
has allowed us to determine the phylogeny and variation of these genes accomplishing both goals
we attempted. Continuing to develop this research, we are analyzing possible correlations between
the variations of a certain paralogs in relation to the phenotype or physical traits of the plant. We
plan to publish the phylogenetic relationships we discovered, as well as any possible correlation
between genotype and phenotype in October 2016. If a correlation can be concluded, these results
and developed primers would be the first marker–assisted breeding available to successfully
determine the drug content of Cannabis before flowering.
During testing our developed primers in June 2015, I began work on my Honor's Thesis to
understand mRNA expression changes during a common chemical treatment used by many growers
to change the sex of the plant for seed production. Through growing female plants and treating some
branches with silver thiosulfate, these plants will produce both male and female flowers, which can
be harvested throughout the growing process. These flowers will be have RNA extracted at three
time points, which will

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