Essay On Soil Detection In Soil

Essay On Soil Detection In Soil
PMTV detection in soil
Soil Samples collection and preparation
Soil samples used in this study were collected from a PMTV infested potato field in North Dakota
in 2016 and 2017. Additionally, comparable soil samples were collected from the nearby field in
2017 where PMTV has never been detected. Collected soil was dried at ambient temperature then
pulverized and stored at cold room (4 ℃). Subsamples of soils were sterilized by autoclaving twice
at 121 C for 60 minutes before storing at 4 ℃.
Soil was artificially contaminated with PMTV using Sporosori of Spongospora Subterranea (Vector
of PMTV). Sporosori of S. Subterranea used in this study was harvested from the surface of infected
potato tuber by scraping with a scalpel followed by ... Show more content on Helpwriting.net ...
2004). One– tube single step RT–PCR assay was carried out in 50 µL reaction mixture using
QIAGEN OneStep RT– PCR kit (Qiagen,Ca). RT–PCR was carried out using a thermal cycler
(T100 thermal cycler, Bio–Rad) to amplify cDNA fragments using the following conditions: RT at
50 °C for 30 min for reverse transcription followed by initial PCR activation for 15 min at 95 °C; 40
cycles of PCR, with each cycle at 94 °C for 60 s, 52 °C (while using PMTV2F and PMTV3 R)or
57°C ( while using C819 and H360 ) for 60 s, and 72 °C for 60 s; and a final extension at 70°C for
10 min. RT–PCR assay products were resolved by standard electrophoresis technique in 1% agarose
gels pre– stained with gel red and the DNA bands were visualized under a UV–transilluminator.
PCR products were cleaned by QIAquick PCR purification Kit (Qiagen) and subjected to Sanger
sequencing (Retrogen, Inc. San Diego, and CA). The sensitivity of RT–PCR technique for detection
of PMTV from soil extracted RNA was determined by using total RNA extracted from series of
spiked soils.
Real time reverse transcription polymerase chain reaction (qRT–PCR)
Attempt was also made to detect PMTV from the soil extracted RNA using qRT–PCR. The primers
and probes were designed targeting coat protein read through protein gene with the help of
sequences obtained from
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Sequency Hereditary Material
INTRODUCTION: Since days bygone, study of living beings required to break barriers of the
single cell and throw light into hereditary material, giving us great insights into nucleic acid
sequences. To face the challenges associated with various questions thrown at biology, great advent
was required to be made in the area of working out the correct order of how nucleic acids are
arranged in an array of genes to give rise to various phenotypes and often, its deviations. Focus was
to be shifted out of the wet laboratory and into silicon chips .Ever since the Thus, arose the
requirement of sequencing the hereditary material, knowing about the entire genetic content of the
organism or rather, it's genome and its analysis. With the help of sequencing a great number of
laboratories across the globe have conducted groundbreaking research and this very important
technique has been established as the basis of a plethora of investigations REASON BEHIND
CHOOSING GENOME ASSEMBLY: From research laboratories to personalized genome analysis,
genome sequencing and downstream processing of the sequenced data has become a mandate for
most biological experimentation. The complete genome sequence of Haemophilus influenzae by
TIGR in 1995 turned a lot of heads with the scope of studying actual relatedness between
organisms,their hereditary material,their genotypic data and biggest of all what advantage we can
derive of them.With the advent of geomic era,or the era of studying not ony

Reflection On Science And Math
Throughout my college experience, there were several things that showed a connection in how
science and math were used to demonstrate my ability to synthesize information on these subjects
and understand different methods of inquiry which were drawn from diverse ways of knowing about
the world and issues that we all face. From these experiences, I was able to use math and science to
communicate how it is implied to the real world and how it can benefit and solve some of these
problems through encouraging healthy lifestyles, equity, and social justice. I was also able to show
how I can turn scientific literature into a creative act of expression and discovery informed by a
scientific article that I translated into an art drawing which was then described in an essay. In a
previous essay that was written in my statistics class I was able to synthesize information on
statistics and understand how its methods were used to real world problems such as the Human
Genome project. The Human Genome Project started in 1990, this project is very beneficial to our
society because it has a positive influence on human health. The project objective is to decode the
DNA sequence and placement of the genes. Researchers collected blood from females and sperm
from males and a total of five people DNA were used for this study. The intentions of the Human
Genome Project were to deliver mapping and sequencing for the human genome and genomes of
model organisms, data gathering and

The Human Genome Project
The author, Francis S. Collins, is the man responsible for the successful completion of Human
Genome Project (HGP). HGP is an international multidisciplinary scientific research project which
was involved in mapping and sequencing human DNA and determining the various aspects of its
function. With this incredible expertise to his credit, Dr. Collins in the book 'The Language of Life'
talks about personalizing medicine by understanding the DNA of each individual. The author starts
by narrating some real life incidents of his family members which threw light on the importance of
DNA sequencing, then the author goes to talk about various situations and conditions which all
implicate the importance of personalized medicine in today's world. In this book, the author focuses
on cancer, microbiome, brain disorders, aging and the genetics related with them. The main
underlying point in explaining the genetics of each of the conditions is to reiterate the importance of
sequencing DNA beforehand so that a personalized medicine for the disease can be developed and
the disease can be treated well before its advanced stage with serious effects.
The book talks about many fascinating facets of DNA and the important message they contain
which when understood can help us to make significant contributions to the field of medicine. The
topic which aroused my interest the most in this book is the last chapter called 'A Vision for the
future'. As the chapter's heading suggests this chapter is

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

Dna Barcoding And Its Effects On The Malaysian Market
There is very little customers can do to ensure that they are purchasing the fish they are paying for.
Producers and restaurants owners have a tendency to mislabel their products for their own reasons.
The main reason is yet to be determined but there are researchers who have made it their goal to
resolve this dispute and show customers what they are truly buying. Too Chin Chin et al. attempt to
utilize the DNA barcoding in the fish segment, to assess the frequency of fish mislabeling on the
Malaysian market (2015). DNA barcoding tries to standardize scientific classification by using
short, single DNA sequence, for example, part of the mitochondrial gene COI to distinguish
between species (Larson, 2007). The process begins with extracting DNA and using primers to
amplify COI regions from the DNA extracts via PCR. The sequences attained are compared to the
available sequences in Bold and GenBank databases to find the mislabeled products. Similarly, a
character–based key can also be constructed to review the reference sequences for variable
nucleotides that can serve as diagnostics for the species you wish to study (Loweinstein, 2009).
Along with Too Chin Chin et al., there are other researchers who based their study on the same
concept to find mislabeled seafood products in certain parts of the world. Dana Miller et al.
examined seafood fraud in two types of Whitefish in Europe. Although, the motivation for these
works are to find mislabeling in products using the standard

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
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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

GH Transgenesis
The inheritance of the GH transgenesis are studied using PCR amplification of the genomic DNA
isolated from fin clips and Sequencing (Figs 3 and 4), and the results are summarized in Table 2.
The two male F1 of opAFP–ccGH, gave inheritance rate of 20% and 16.67%, respectively. The two
male F1 of rtMT–ccGH, gave inheritance of 10% and 36%, respectively. Our results indicated that
the inheritance of the GH transgenesis by the F2 generation, 10% to 36%, suggesting that the F1
might be mosaic (Table 2).
Transfer of channel catfish growth hormone (ccGH) cDNA to F2 channel catfish has imparted
enhanced growth rate (Fig. 5). At 12 weeks old and under laboratory conditions, the largest
transgenic opAFP–ccGH was 2.3 times that of the average non–transgenic ... Show more content on
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10a). At 12 weeks transgenic channel catfish containing channel catfish Ictalurus punctatus growth
hormone (ccGH) cDNA, driven by the ocean pout Zoarces americanus antifreeze protein promoter
(opAFP), opAFP–ccGH, grew 1.4 to 1.6 fold larger than their non–transgenic siblings, and
transgenic channel catfish containing channel catfish growth hormone (ccGH) cDNA, driven by the
rainbow trout Oncorhynchus mykiss metallothionein promoter (rtMT), rtMT–ccGH, grew 1.35 to
1.8 fold larger than their non–transgenic siblings (Table 2; Fig. 10a) (P < 0.0001). However, there is
no significant between transgenic of opAFP–ccGH family number 1 and non–transgenic rtMT–
ccGH family number 2, and no significant between transgenic of rtMT–ccGH family number 1 and
non–transgenic opAFP–ccGH family number 2 (Fig. 10a), probably due to the family effect. There
is always a significant difference between mean body length of transgenesis and their non–
transgenic siblings (Table 3; Fig. 10b). However, there is no significant difference between
transgenic of rtMT–ccGH family number 1 and non–transgenic rtMT–ccGH family number 2, and
non–transgenic of both families of opAFP–ccGH (Fig. 10b). The body weight and length were
highly correlated (P < 0.01) in both genotypes in both families. Our results indicated that to develop
a fast growing channel catfish we need combine the transgenic ccGH by

Why It Is Still Considerate As The Gold Standard For Dna...
This technique is still very useful overall because of its low error range, and also is the reason why it
is still considerate as the Gold standard for DNA sequencing, among other things to validate NGS
data (Pareek & Smoczynski 2011).
Aiming to reduce costs and improve quality and efficiency, the New Generation Sequencers
appeared. With the surging of NGS technologies, today it is viable to sequence in a particular
subject with a suspected genetic disease or with tendency to that compound disease, up to thousands
of genes at the same time (Pareek & Smoczynski 2011). There are different existing methods,
however all shared similar features about Massive Parallel sequencing reactions. All of them
required a pre–determined library sample preparation through DNA break–up and amplification by
custom adaptors. Each library fragment is amplified on a solid surface (cell flow) by covalent–
attached DNA linkers (oligonucleotides) which hybridize the library adaptors. This amplification
creates millions of DNA clusters, each originated from a single library fragment. Each fragment will
act as a single sequencing reaction. After this, each machine provides a raw data at the end of the
sequencing run. This run data is a collection of DNA sequences that were generated of each cluster.
At the moment, the most broadly used targeted sequencing method is maybe the Whole Exome
Sequencing (WES) since is the known genome protein–coding region and represents no more than
2% of the genetic

A Horse 's Gastrointestinal Tract
Horses are monogstric animals with a relatively small stomach. From the horse's mouth to their
large intestine, their gastrointestinal tract is similar to that of a human's. However, past the cecum, a
horse's gastrointestinal tract is more similar to a cow's [3]. A horse's gastrointestinal tract can be
divided into three segments: foregut, midgut, and hindgut [4]. The foregut consists of the esophagus
and stomach. Once food has passed through the stomach, it enters the small intestine (midgut):
duodenum, jejunum, and ileum, which join the hindgut, cecum, colon, and rectum, at the ileocecal
junction. The small intestine and stomach can almost receive a continuous flow of food [3]. The
cecum is a large fermentation vat located on the right side of the animal. Carbohydrates fermented
by fibrolytic bacteria produce volatile fatty acids, which account for 60–70% of the their energy.
However, in modern management practices, horse owners and equine caretakers do not let horses
graze like they naturally should; therefore, they substitute the horse's diet with grains and fats,
which the horse is not designed to properly digest. This unbalanced feeding regimen causes
numerous digestive disturbances [3].
Horses are classified as hindgut fermenters, meaning a balance of good and bad bacteria aid in the
digestion of foodstuff in the cecum and large intestine [5]. The hindgut is not only a fermentation
vat, but it also stimulates the immune responses, protects against pathogens,

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

A Research Study On Scar Markers
SCAR markers are PCR based primers that represent genomic DNA fragments at genetically
defined loci, that are identified by PCR amplification using sequence specific oligonuceotide
primers (Paran and Michelmore, 1993; Me Dermott et al., 1994). Inception of SCARs involves
cloning the amplified products of arbitrary marker techniques and then sequencing the 2 ends of the
cloned products. The sequence s therefore used to design specific primer pairs of 15–30 bp which
will amplify single major bands of the size similar to that of the cloned fragment.
The greater the variation in DNA sequence, the easier it is to generate polymorphic markers.
Therefore the plant species used for SCAR development should have sufficient variation for te traits
of interest at both the DNA sequence and phenotypic levels. Researchers over the years have
employed various non–sequence primed PCR markers to develop SCAR markers for the
identification of sex in dioecious species of crop plants.
Chromosomes and its sex determining genes have driven genetic control of sex determination in
dioecious crops. In dioecious crops a vast variability has been seen in the genetically controlled sex
determination and a DNA polymorphism has been mainly attributed, that are directly involved in
expression of particular sexual phenotpe (Aryal and Ming, 2013). In dioecious crops either one of
the crops will be of great agricultural or commercial interests like Simmondsia chinensis,
Hippophae rhamnoides. In Garcinia

The Dna Samples Of Gophers Tested
Background
The DNA samples of gophers tested are prime examples of evolution. There are several
evolutionary processes that occurred with the species being study. Speciation occurred once a river
causing their gene pools to diverge separated the gophers. This evolutionary occurrence represents
allopathic speciation. Furthermore, once the species' gene pool diverged the morphological species
concept could be observed. The Geomys attwateri is slightly larger than the Geomys brevicep by 10
mm. During this evolutionary occurrence reproductive isolation may have occurred as well. Due to
the species being isolated geologically, interbreeding no longer occurred separating the gene flow of
each population. If these species were able to breed ... Show more content on Helpwriting.net ...
Campbell) Although morphological observations help identify species they are not as accurate as
testing the DNA of species with similar resemblance. The most accurate way to identify species is to
extract their DNA and use bioinformatics. To decipher if a species by its morphology can be
suggested as a hypothesis, but the results of its DNA will identify the species accurately. Tissues
samples can be taken from the species in question, and the DNA can be extracted from tissue. Once
the DNA is extracted it can be amplified. DNA can be amplified by the PCR procedure, in which
specific gene regions can be used as barcodes to identify the species. These specific regions are
known as Cytochrome oxidase 1 and Cytochrome B. Once these regions are purified and amplified,
the samples can be sequenced, and the species can be identified. These procedures can solve many
mysteries and questions. The DNA sequencing of different species can identify where it falls on the
phylogenetic tree and where the population separated to produce a new species. These procedures
help us understand the evolution of ancestors to the present and the connection between each
species. Two separate species with multiple similarities can be observed, and bioinformatics can
help answer that question.
Purpose
There are several experiments that must be conducted before a species can be identified. The tissue
samples of these organisms must be obtained, and their tissues must

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

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

Evolution Of The Human Genome Project
While many diseases and viruses are caused by outside sources, some diseases occur from within
the human body. Regular ailments can be cured with medicine, or fought off overtime by getting a
vaccine, but certain diseases and anomalies cannot be directly treated. This is because they are
genetically inherited by certain parts of one's DNA. DNA stands for Deoxyribonucleic Acid, and is
inherited from the parents of a person. These strands, found within the nucleus of all cells,
determine the appearance and genetic structure of a person. Through one's DNA, there may be
diseases inherited from the parents, such as sickle cell anemia, Gaucher's disease and Parkinson's
disease. In order to heal and fix patients, doctors needed to learn more about the Human Genome. In
1990 work began on the Human Genome Project, which would map the entirety of the genes in the
human species. However, the participants would not have been able to work without the discoveries
made by those before them. In order for The Human Genome Project to exist, the background of
genetics must be known, for the discoveries made in the field would be what eventually led the
project itself. Genetics in itself is a fairly new concept, which officially began in 1865 in central
Europe. A monk named Gregor Mendel learned about heredity and inheritance through breeding pea
plants. After retiring from his teaching and scientific life, he became the abbot of his church.
Unfortunately, the importance of his discovery was

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

Human Genome Project Essay
Human Genome Project Essay
The Human Genome Initiative is a worldwide research effort that has the goal of analyzing the
sequence of human DNA and determining the location of all human genes. Begun in 1990, the U.S.
Human Genome project was originally planned to last 15 years but now is projected to be complete
in 13 years. This project was started to find the 80,000 – 100,000 human genes and to determine the
sequence of the 3 – billion chemical bases that make up human DNA. The information generated by
the human genome project is expected to be the source book for biomedical fields, including those
such as developmental biology and neurobiology, where scientists are just beginning to understand
the underlying molecular mechanisms. The ... Show more content on Helpwriting.net ...
In the spring of 1987, a report on the human genome initiative was prepared by the Health and
Environmental Research Advisory Committee (HERAC) of the Department of Energy (DOE). In
early 1988, further discussion culminated in the publication of two additional, widely circulated,
influential reports. The U.S. Congress Office of Technology Assessment (OTA) report presented a
comprehensive and detailed analysis of the scientific developments that had led to the promise of
"mapping and sequencing" the human genome and presented an outline for a multi–phase research
plan for accomplishing the goal of sequencing human DNA over the course of the following two
decades. In fiscal year 1988, the Congress of the United States launched the human genome project
by appropriating funds to both the DOE and the National Institutes of Health (NIH) specifically for
support of research efforts to determine the structure of complex genomes. The NIH was delegated
$17.2 million and the DOE received $10.7 million in 1988 by the human genome research institute.
It is generally agreed that the overall goal of the Human Genome Initiative is to acquire fundamental
information needed to further our basic scientific understanding of human genetics and of the role of
various genes in health and disease. As refined through the discussions over the last half of the
1980's and defined in the NRC report, the Human Genome Initiative has several interrelated goals:
Construction of a

The Human Genome Project and Patenting DNA Essay
The Human Genome Project: Patenting DNA
The Human Genome Project is a global initiative to map the approximately 100,000 genes present
in the genome of humans. Planning for the project was started in 1989 with a proposal submitted by
the Office of Technology Assessment and the National Research Council. In 1990, the actual project
began under the joint leadership of the National Institutes of Health and the Department of Energy.
The goals of the project are as follows:
Mapping and sequencing the human genome
Mapping and sequencing the genomes of model organisms
Data collection and distribution
Ethical, legal, and social consideration
Research training
Technology development
Technology transfer
Originally, research ... Show more content on Helpwriting.net ...
The downside of this "genome mania" is high expectations. Current market values of life science
companies are very high. Companies are faced with a lot of pressure from shareholders to provide
new blockbuster therapies that will net those investors large profits. The problem with this mentality
is that research takes a lot of time and a lot of money (2). The fear of some researchers is that
industry will not be open with the results of their genome research, sequestering away nucleic acid
sequences in private databases, or tying up huge amounts of information in pending patents. This
goes against the original aim of the project which was to place all information gathered in free,
publicly accessible databases. Recent developments in the Human Genome Project only heightened
these fears.
On May 9, 1998, Crag Venter, president of The Institute for Genomic Research (TIGR), announced
his company was teaming up with pharmaceutical giant Perkin–Elmer to sequence the human
genome in just three years (3). This news took the genetics community by storm. The original plan
called for a single, cohesive strategy to thoroughly map the human genome in a linear method. The
new Perkin–Elmer/TIGR partnership planned to sequence the genome with a new method called
whole genome shotgun sequencing. By this method, DNA would be chopped up, sequenced all at
once, and supercomputers would be used to assemble the

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

The Human Genome Project : A Research Project
The human genome project is a research project which had a purpose of being able to map and
understand all the genes of human beings and organisms (National Human Genome Research
Institute, National Institutes of Health 2014a) and to determine the DNA sequence of the complete
genome (National Human Genome Research Institute, National Institutes of Health 2014b). The
Human genome project enabled researchers to obtain the instructions they needed to gain an
understanding of how to build an individual (Genetics Home Reference 2014a). The Human
Genome Project made several claims which included to complete sequencing and mapping the
genomes of organisms and the ethical, legal and social consideration related to it. (U.S. DOE
Human Genome ... Show more content on Helpwriting.net ...
To sequence DNA it needs to be amplified first and this can be done in two ways; The Polymerase
Chain reaction (PCR) and Cloning. Cloning isolates the DNA fragments from restriction enzymes
and then combines the fragments with the vector. Once united with the vector the DNA fragments
are then able to replicate to provide an unlimited amount of DNA for the experiment. PCR allows
DNA to be multiplied millions of times in a couple of hours, PCR is used because it's highly
specific, easily automated and can amplify very small samples of DNA. The technique of PCR has
had a huge effect on genetic disease diagnosis. To sequence the DNA, Gel Electrophoresis is used as
it separates DNA fragments according to their size by running an electric current through the gel
(Boehm). Mapping and sequencing the genome of organisms has allowed tests to be conducted, for
example; gene tests, this is where individual genes or short lengths of DNA or RNA are tested for
and Chromosome tests; this is where whole chromosomes or long lengths of DNA are tested for
(National Human Genome Research Institute, National Institutes of Health 2014c).
This claim has been met by the human genome project, this is because by mapping and sequencing
the genomes of standard organisms genetic testing and genetic screening can be conducted. For
example, new

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
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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),

Dna Sequences Using Polymerase Chain Reaction
Amplification of 16S Ribosomal DNA Sequences using Polymerase Chain Reaction
Edwina Abou Haidar,
Houssam Al Koussa,
Mary AbedAlAhad.
Department of Biology, Lebanese American University, Byblos, Lebanon
Abstract The 16s rRNA gene sequencing is a widely common amplicon sequencing method used to
identify and compare bacteria in a given sample. This method is well established and allows to study
phylogeny and taxonomy of complex microbiomes. In this study, an unknown sample of extracted
microbial DNA was analyzed by performing the polymerase chain reaction followed by agarose gel
electrophoresis. The results were accurate since three distinct bands (1500 basepairs) corresponded
to our sample (duplicates) and the positive control. This indicates clearly the amplification of the
16s rRNA gene whose further sequencing technique constitutes a pivotal tool in the accurate
identification of bacterial isolates as well as the discovery of novel bacteria in clinical microbiology
laboratories.
Abbreviations
rDNA: ribosomal DNA rRNA: ribosomal RNA bp: base pair
PCR: Polymerase Chain Reaction Introduction Physiological and biochemical tests constituting the
basis of conventional differentiation between bacterial species are somehow cumbersome, consume
a lot of time and require different approaches [1]. Furthermore, the commercial identification
systems failed to identify commonly encountered bacteria and uncommon isolates. In fact, these
commercial systems

Ecology And Plant Ecology
In this article examples are going to be discussed of the application of molecular biology in the field
of plant ecology, what molecular biology is as well as what plant ecology is. Plant ecology is one of
the branches in the scientific field of ecology that mainly focus on plant population and their
surroundings (McMahon, 2016). Plant ecologists also look at other factors that have an impact on
the plants and their environment. According to the MIT Department of Biology, plant molecular
biology is the study where biological data such as plants genetics, genomes, biochemical and the
cell biologics is inserted into computers to understand the development, growth and physiology of
plants at a molecular level. The examples that is going to be ... Show more content on
Helpwriting.net ...
Researchers do not just look at the plant but keeps in mind how the plants interact with each other
and their environment. A Plant ecologist do not just look at plants but also the soil conditions,
animals and other influences that might have an impact on the plants environment. According to
McMahon (2016) plant ecology is not just a plant itself but, is everything from understanding the
plants environment functions as well as the interaction of humans with the natural environment. The
area most focused on in plant ecology is topics like climate change, plant diseases and the symbiotic
relationship between plant species and how plants spread in nature (McMahon, 2016). Plant ecology
involves a lot of field work because the plant needs to be viewed in their natural habitat to
understand why the plant looks like it does. Plant ecology covers a wide range of research for
instance the study of plants growing in a specific ecosystem for example the rainforest, or a specific
area that is of interest, like a population of plants that is growing next to a polluted river or dam. It
can also help researchers to study endangered ecosystems and plant populations including not
vascular plants like mosses. Plants make up a very large part of the natural environment. Plants do
not just provide people and animals with food but also with shelter for animals, prevents erosion and
the most important part is that plants provide us with oxygen (McMahon,

Outline Of The AFLP Procedure (RFLP)
Figure 7. Outline of the AFLP procedure (Vuylsteke et al., 2007)
(2) Restriction fragment length polymorphisms (RFLP)
When utilizing PCR–RFLP, a DNA fragment is first amplified by PCR, then it is digested by a
certain restriction endonuclease to generate a restriction polymorphic profile for the test subject
species (Shaw et al., 2002). PCR amplification should be highly conserved among a species so that
it can be easily amplified. Each fragment length is considered an allele, and RFLP occurs when the
length of a detected fragment varies between individuals.
(3) Random amplified polymorphic DNA (RAPD)
RAPD is effective in screening the differences in DNA sequences. The RAPD markers are also
DNA fragments from PCR amplification,

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

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

Origin : Bacterial And Archaeal Adaptive Mechansim Essay
Background
Origin: Bacterial and Archaeal Adaptive Mechansim
CRISPR loci are first identified in archaea and bacteria when they systematically drew attention
from scientists with their biological function to fight phages and viruses (Hsu, Lander, Zhang,
2014). Structurally, a clustered set of Cas (CRISPR–associated) genes and a unique CRISPR array
constitute the CRISPR loci. The CRISPR array was further comprised of short repetitive sequence
interspaced by distinctive sequences (spacers) in correspondence with exogenous genetic bits
(protospacer). The natural CRISPR systems in bacteria and archaea carried out their adaptive
antiviral immunity by following a three–step mechanism, namely acquisition of spacers, crRNA
biogenesis, and interference (Wright, Nuñez, Doudna, 2016).
The infection by undocumented DNA starts the acquisition of viral DNA. Upon the detection of the
invasion of bacteriophages, bacteria defend themselves in a timely fashion by inserting bits of viral
DNA, the protospacer, into their chromosome at the end of CRISPR locus (Wright, Nuñez, Doudna,
2016). To maintain the structure of CRISPR array, bacteria initiate the replication of a repetitive
DNA sequence, the repeat (Barrangou et al., 2007).
Next, crRNA biogenesis takes place in two stages. First, the CRISPR array and the Cas gene are
transcribed respectively into a single pre–crRNA and Cas proteins. In this process, different types of
CRISPR systems are unique in their Cas proteins they encode.

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

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

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

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

The Power Of Modifying Genetics
The power of modifying genetics is at our fingertips, allowing us to change the genes of living
creatures, which of course includes humans. The concern is; what genes should be modified, and
which genes should be left alone. A company called 23andMe, named after the 23 pairs of
chromosomes in a human cell, will provide ancestry genetic reports and uninterpreted raw genetic
data using only a kit. Created in 2006, out of Mountain View, California, the company specializes in
three different products or kits, an ancestry edition, a health edition, and a complete edition. Sadly,
due to FDA regulations and complications, 23andMe has had to sideline the interpretation of their
health–based products in the United States. Currently, 23andMe mainly ... Show more content on
Helpwriting.net ...
DNA DTC is a company whose genetic products and services includes research, exome sequencing,
and whole genome sequencing, but tests carry a steep price tag. Another company, Genelex is
different from the previous companies, and specializes in paternity and pharmacogenomics, which
simplified, is the study of individualized effect of drugs based on genetics. Genelex and other
companies similar to them could be a threat by repositioning themselves, to combat health based
genomic sequencing.
A target market is a business going after a certain group of people based on age, sex, race, location,
religion, and other factors. My estimated target market for 23andMe is new families, and I will
explain why. During the pregnancy process, numerous tests are performed on the unborn baby as
well as the bearing mother to determine factors like complications or growth. If additional tests, like
23andMe's genetic testing, could be performed to determine more about not only the baby, but also
themselves, it is advantageous for both parties. In a new family, roles are being set, someone is
becoming a father, someone is becoming a mother, and a newborn is becoming a toddler. In that
emotional time, parents will want to use genomic research to make sure they can continue to be a
mother or father to their children, and that nothing from their genetics will impair or limit the child.
Relative

Essay On Adaptor Ligated DNA
beads to remove any unwanted ligated products.
The universal and indexed sequences were amplified by PCR using adaptor–ligated DNA
fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext
Multiplex Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex Oligos
for Illumina. Once the PCR was done, the adaptor–ligated DNA was cleaned up using AMPure XP
beads to remove any unwanted products. Figure 3: Pre–Sequencing Sample Preparation. Samples
were prepared and amplified on a Biomek 4000 before sequencing
The libraries were checked for quality with the Agilent 2100 Bioanalyzer High–Sensitivity. The
bioanalyzer results confirmed a successful isolation and pre–sequencing preparation of ... Show
Fragments that result primarily from heavy digest conditions are known as "resistant" to MNase
digestion. "Sensitive" nucleosomes, on the other hand, are easily released by MNase, and so these
mononucleosomally protected fragments are found predominately in the light digest (these
fragments become <150 base pairs (bp) in a heavy digest).
Sensitivities and Positions of Nucleosomes
Nucleosome sensitivities displayed using heatmaps that show the differences between the number of
fragments produced in the heavy and the light digests, sorted on max with 5 clusters. Nucleosome
position for each sample was mapped onto a heatmap of the combined number of fragments
produced in the heavy and light digests, sorted with kmeans with 8 clusters. These maps enabled
identification of nucleosome characteristics for enriched genes from the cells from the 0–hour time
point.
12 Hours 24 Hours 36 Hours 0 Hours
Figure 5: Nucleosome Sensitivity and Occupancy Heatmaps. The heatmaps depict the difference
between the number of mononucleosomally–protected fragments under light and heavy digest
conditions at the various time points. A 1000 bp on either side of a TSS for 20,000 human genes are
displayed on each heatmap. The yellow indicates sensitive nucleosomes while the blue areas

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
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

Alu Sequence Lab Report
Kearra Barretto
Dr. Rupa Tuan
BIO–1103–L–04: General Biology II Lab
25 April 2018
The Presence of the Alu Sequence Using PCR
Introduction
For millions of years, repetitive DNA sequences such as the "Alu sequence" have been randomly
inserted in the human genome. In this experiment, I will study whether or not the repetitive element
such as the "Alu sequence" is present in the PV92 region of chromosome 16 of my DNA. I will then
gather the data from my Biology Lab Class and compare it with those of the United States. To
perform this experiment, the method of Polymerase Chain Reaction (PCR) will be used to amplify
the DNA. The purpose of using PCR is to create enough mass in order for it to run on the agarose
gel electrophoresis. Performing this ... Show more content on Helpwriting.net ...
After it was expelled back into the cup, 1 ml of the saline rise was transferred into a micro test tube
in order for it to be spun in a balanced centrifuge. The micro test tube that contained the 1 ml of
saline rise was inside of the centrifuge for 2 minutes, resulting in cells at the bottom of the tube.
Since all of the cells were present at the bottom of the tube, the saline was poured off and the tube
was vortexed to be sure that there were no clumps of cells. Afterward, the InstaGene Master Mix
(which removes cofactor to inhibit DNA cutting enzymes) was vortexed with the saline rise in order
to fully mix the contents of the tube (Bio–Rad Laboratories, Chromosome 16: PV92 PCR). The tube
was then incubated at 56 degrees Celsius for 10 minutes to inactivate DNAses and put on a second
heat block at 100 degrees Celsius for 5 minutes to disrupt cell membranes. The tubes were put into a
centrifuge then cooled down in a 4 degrees' Celsius fridge.
PCR
20 ul of DNA was added to 20ul of Master Mix. The Master Mix contained primers, dNTPs, Mg2+,
Taq DNA polymerase, and yellow dye. Both the DNA and Master Mix were mixed with the
micropipette. The DNA was then put into the thermal cycler containing 40 cycles of PCR
amplification, amounting to 3.5 hours of amplification.
Gel

Eimeria
In which 50 µl of PCR master mix used for amplification of ITS1 region .
Also (5μl) of DNA template that extracted from stool samles was added then 1.5 μl of each type of
Primers(forward and reverse)added to the master mix and then blend well using Exispin vortex
centrifuge ,then this tubes would transferred to the Thermocycler machine, which has been
programmed by the previous program for amplified of ITS1 region.The PCR products were
electrophoresed in agarose gel and visualized on UV trans illuminator and then photographed using
photo documentation .
2.5–Measurement of DNA Concentration We have measured the DNA concentration of fifteen
samples (five samples to each one of the three species of Eimeria) that extracted and containing on
ITS1 region which amplified in the PCR process before sent to determine the sequences of the DNA
of the three Eimeria species which causing poultry coccidiosis by using of (Nanodrop machine) all
selected samples gave more than 100 concentration ng / ml, which consider the lowest concentration
required in the process of identifying DNA sequences [13].
2.6–DNA sequencing methods ... Show more content on Helpwriting.net ...
(5258bp) PCR product of the species E.tenella ,) 501 bp) PCR product of species E.necatrix and
(503bp) PCR product of the species E.maxima were purified from agarose gel by using (EZ EZ–10
Spin Column DNA Gel Extraction Kit, Biobasic. Canada). The purified ITS1 region from PCR
product samples were sent to Bioneer Company in Korea for performed the DNA sequencing (AB
DNA sequencing

CRISPR Array
Origin and Development of CRISPR–Cas9 System
CRISPR loci are first identified in archaea and bacteria when they systematically drew attention
from scientists with their biological function to fight phages and viruses (Hsu, Lander, Zhang,
2014). Structurally, a clustered set of Cas (CRISPR–associated) genes and a unique CRISPR array
constitute the CRISPR loci. The CRISPR array was further comprised of short repetitive sequence
interspaced by distinctive sequences (spacers) in correspondence with exogenous genetic bits
(protospacer). The natural CRISPR systems in bacteria and archaea carried out their adaptive
antiviral immunity by following a three–step mechanism, namely acquisition of spacers, crRNA
biogenesis, and interference (Wright, Nuñez, Doudna, 2016).
The infection by undocumented DNA starts the acquisition of viral DNA. Upon the detection of the
invasion of bacteriophages, bacteria defend themselves in a timely fashion by inserting bits of viral
DNA, the protospacer, into their chromosome at the end of CRISPR locus (Wright, Nuñez, Doudna,
2016). To maintain the structure of CRISPR array, bacteria initiate the replication of a repetitive
DNA sequence, the repeat (Barrangou et al., 2007).
Next, crRNA biogenesis takes place in two stages. First, the CRISPR array and the Cas gene are
transcribed respectively into a single pre–crRNA and Cas proteins. In this process, different types of
CRISPR systems are unique in their Cas proteins they encode. Specifically, type II

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
content on Helpwriting.net ...
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

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