Examples Of Epigenetics

Examples Of Epigenetics
Example of epigenetics...Epigenetics play a large role in the expression of certain genes. Through
particular changes in the environment and genetic information, similar genomes can result in
different organisms with very diverse features. Chromatin modification involves the regulation of
genes by alterations, or specific additions, to chromatin. Unlike mutations, these modifications do
not directly involve the nucleotide sequence and can be easily reversed. The presence of certain
modifications can impact chromatin configuration and the recruitment of enzyme complexes to
control DNA. Regulation of chromatin structure is a fundamental process that largely influences
epigenetic inheritance through histone modifications, DNA methylation, and nucleosome ... Show
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During methylation, methyl groups (CH3) are attached to histone tails with the aid of histone
methyltransferases (HMTs). These proteins transfer one, two, or three methyl groups from S–
adenosyl–L–methionine to lysine or arginine residues. Lysine methylation involves a lysine
methyltransferase that specifically targets and methylates lysine within the N–terminal tails.
Similarly, arginine methylation occurs through the transfer of methyl groups from SAM to the ɯ–
guanidino group of arginine. Although histone methylation does not change the charge of residues
and does not greatly impact nucleosome interactions for chromatin folding, it results in binding sites
for certain enzymes, which enables the regulation of chromatin condensation and nucleosome
mobility. Methylation can also block the binding of proteins that interact with unmethylated histones
and inhibit other modifications. Therefore, histone methylation regulates genes by promoting the
binding of positive transcription factors and by blocking the attachment of negative transcription
factors. However, some methylations can prevent gene transcription by mediating heterochromatin
formation. For example, H3–K9 and H3–K27 methylation silences gene expression at certain
euchromatic
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A Study Of Dynamic Regulation Of Gene Expression Essay
The majority of cells in the human body are not human at all. The 100 trillion prokaryotic cells that
make up our microbiota, constitute 90% of the cells in our bodies, and are derived from more than
40,000 bacterial strains (Forsythe & Kunze, 2012). Bacterial cells reside in animal hosts as
commensals, symbionts, or as pathogenic parasites, forming a veneer over almost all body surfaces
(Dave et al., 2012). Increasingly, research is showing the importance of host microbiota composition
and the bidirectional signaling pathways between the brain and the gut, some of which are
epigenetic. These studies elucidate the profound impacts that signaling pathways, such as short–
chain fatty acid mediated effects, nucleomodulins, and other bacterial metabolites, can have on
health, behavior and cognition (Sommer & Backhed, 2013). 'Epigenetics,' derived from the Greek
root 'epi ' meaning on top of, is the study of dynamic regulation of gene expression due to factors
that act on chromatin structure, nuclear architecture and other molecular events that do not change
the DNA sequence (Stilling et al., 2014). In addition, epigenetics has sometimes been defined as
sequence– independent heritable changes in gene expression (Holliday, 1987). Epigenetic processes
include post–translational histone modification, as well as cytosine methylation and interactions of
non–coding RNAs (Jaenisch & Bird, 2003; Landry et al., 2013). Post–translational histone
acetylation results in a decreased

The Importance Of Chromosomes And Chromosomal Structure
The vast majority of the scientific community is cognizant of the importance of chromosomes and
chromosomal structure in cellular replication and lifespan. One of the most prominent and greatly
researched discoveries of chromosomes has been the telomere and the enzyme telomerase with
which telomeres interact. The term telomere refers to the caps located on the ends of chromosomes
as a form of protection against chromosomal shortening and aging. Telomerase is an enzyme that
aids in the lengthening of telomeres through replenishing TTAGGG ribonucleic repeats that do not
code for particular amino acids and is present in high amounts exclusively in cells such as gametes
or stem cells. These repeats then undergo chromosomal shortening rather than the necessary
ribonucleic acid sequences of DNA. (Yuanjun et al., 2014). Telomerase itself is a highly intricate
enzyme that is capable of interacting with accessory proteins, RNA templates, and the
ribonucleoprotein complex of a catalytic human reverse transcriptase. The human telomerase gene
commonly referred to as hTERT is responsible for activating telomerase and is further regulated by
transcription factors. Copious studies have revealed that aging and other growth crises such as
cancer is telomere length dependent and may be avoided through the increased expression of the
hTERT gene, telomerase activity, and stabilization of telomere length. (Degerman et al., 2011).
Aging is additionally avoided in cells through the negation of

Macrohih2a1 Case Study
MacroH2A1.1–overexpressing cells display ameliorated glucose metabolism, 214 reduced
expression of lipogenic genes and fatty acid content (40). These associative 215 studies indicate a
possible conserved involvement of macroH2A1 isoforms, in lipid 216 metabolism. A number of
mechanistic studies using animal have explored this 217 possibility, yielding conflicting outcomes
(Table II). Two mouse models with a 218 macroH2A1 knockout have been reported under a
standard diet feeding. In the first 219 model, generated in the pure C57Bl/6J background,
developmental changes in 220 macroH2A1–mediated gene regulation were observed (42): up–
regulation of 221 lipogenic genes was detected in the liver of the knockout mice (42), which
displayed 222 ... Show more content on Helpwriting.net ...
The changes in lipogenic gene expression 226 have subsequently been associated with differential
physical occupancy of the gene 227 body by macroH2A1 (42, 43). In the second model, knockout of
macroH2A1 in a 228 mixed background led to a variable hepatic lipid accumulation in 50% of the
229 females (44). In this model, the X–linked thyroxine–binding globulin (Tbg) gene was 230 found
to be upregulated in steatotic livers. Tbg is the main carrier of the thyroid 231 hormone T4
(thyroxine), a major regulator of energy metabolism, which could be 232 responsible for the
enhanced fat accumulation. Enrichment of macroH2A1 at the 233 Tbg promoter in female animals
indicated that increased Tbg expression in 234 macroH2A1–knockout mice could be a direct
consequence of the absence of this 235 histone (44). In contrast, our analysis of the in vivo role of
macroH2A1 in response to 236 nutritional excess led us to discover that genetic eviction of
macroH2A1 confers 237 protection against high fat diet–induced obesity and metabolic
derangements in 238 mice (45). Together, these mice studies did not address the role of the single
239 macroH2A1 isoforms; moreover if these histone variants can impact energy 240 turnover in
extra–hepatic depots, was unknown until recently. In the skeletal 241

E. Coli Pglo Lab Report
Introduction
Scientists can study and manipulate genes by using precisely engineered plasmids, According to
ADDGENE, a nonprofit plasmid repository, plasmids "have become possibly the most ubiquitous
tools in the molecular biologist's toolbox" ("What Is a Plasmid?"). In this experiment, we will use
pGLO to genetically transform the bacteria E. coli. pGLO is a genetically engineered plasmid that
carries the reporter genes for both green fluorescent proteins (GFP) and the ampicillin resistance.
GFP, a protein typically found in the bioluminescent jellyfish Aequorea victoria, exhibits a bright
green fluorescence in the presence of blue to UV wavelengths (Mecham); the protein absorbs UV
light from the sun and emits it as a lower energy green light, exemplifying the second law of ...
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The gene for GFP is regulated by an inducible repressor system, meaning it is turned on by
environmental factors. In this case, GFP is expressed when exposed to the sugar arabinose;
moreover, the organism will glow only when arabinose is present. Without arabinose, the repressor
attaches to the regulator/ operator segment of the gene and acts as a roadblock, preventing RNA
polymerase (RNAP) from reading the structural gene and creating a complementary mRNA strand;
thus, GFP protein production is prohibited. However, when present, arabinose binds to the repressor,
changing its active site, so it can no longer bind to the operon; RNAP can then initiate the
transcription of the GFP gene by binding to the promoter segment. Thus, I predict that the E. coli
will glow only when pGLO and arabinose are present because arabinose activates the expression of
GFP, a gene found in pGLO. Regulation of gene expression is crucial to prevent wasteful
overproduction of unneeded proteins and to allow adaptation to new environments (Regulation of

How Dna Is Influenced By The External Environment
Does "DNA (genes) control you?" Or is it the environment? Your internal gene pool is not only just
DNA that was inherited from your elders but it's a combination of your inherited material but also a
daily dose of your external environment. Most of your genes switch on or off with the aid of
external stimuli, which is how your 725 Mb genetic setup influenced by your own surroundings.
Today we will talk about some ways how your genetic setup is influenced by the relative external
environment.
Transcription factors – Environmental Pollutants can affect the DNA sequence by changing the
transcription factors, which play an important role for initiation of central dogma to express
respective gene. During transcription these factors have DNA binding sites ... Show more content on
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For example, depression is caused by regular drinking of alcohol. It is due to low folate levels which
in turn controls by (TACE) a specific gene, not to help another gene (MTHFR) make enough of its
protein. Too little of this protein changes the level of folate (another protein) in our blood, and this
may cause depression.
Chemicals – Some chemicals are also not good for your health even many of these may change your
DNA sequence permanently so can be heritable. Same way there are certain chemicals which affect
gene expression involved at the time of development. Cyclops fish are a well–studied example of
the way in which an environmental chemical MgCl2 can affect expression of genes involved in eye
development Temperature – In some organisms outside weather may also influence their own
running genetic channel. This may also modulate gene expression in certain organisms. For example
C gene carries by Himalayan rabbits, which have role in development of pigments in the fur and
eyes, and whose expression is regulated by

Being Confused With Mechanisms For An Organism 's Genome
Since the word epigenetics was coined by Conrad Waddington in the 1940's, the term has been used
largely to describe phenotypic changes that do not adhere to the typical Mendelian inheritance
expectations for an organism's genome (Waddington C, 1942). To put it simply the term referrers to
intrinsic or extrinsic forces that alter expected visible changes in an organism and these changes are
often heritable by offspring (NIH, 2015). This should not be confused with mechanisms such as
point mutations which also can alter genes by producing a different genotype, but rather should be
thought of as a change in state of genetic material leading to alterations in the expression potential
of a cell and its substrates (Ledford H, 2008). Genes are the blueprints of every organism and as
such they specificity lay out the formation and function of that organism and everything within it.
These same genes are what is passed on to offspring and thus are considered heritable. However,
since most organisms obtain two sets of these blueprints, one from each parent, the genotype and
thus phenotype are not always a clear cut predictable outcome due to mechanisms such as crossing
over, chromatin remodeling or even epigenetics. Genes are stretches of deoxyribonucleic acids
(DNA) that encode ribonucleic acids (RNA) that in the end encode for a polypeptide or chain of
polyepties that have a specific function in the organism such as regulation or expression (Alberts B,
2002). Epigenetics can

Lncrna Essay
As a pivotal component of regulation in the biological process, long non–coding RNA also known
as "junk–DNA," provides additional insight on the function of RNA in gene expression. Though
lncRNA does not code for proteins, it's role in the regulation of transcripts certifies its complexity in
cellular activity. (Rinn and Chang, 2012). Containing more than 200 nucleotides, it was first
transcribed from enhancer regions and identified to have notable roles in cis– and trans– regulation
which are equally involved in gene activity. Its location has been identified in introns or within
genes (Milligan and Lipovich, 2014). The most appealing features of lncRNA is its ratification of
secondary and tertiary structures. Jacob and Monod proposed ... Show more content on
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In Archetype II lncRNA works to titrate proteins and protein factors away from chromatins, yet
titrating them into nuclear subdomains while serving as decoys. This is common in miRNA sites
where lncRNA appears as decoys. Acting as guides in Archetype III, lncRNA functions in either cis
or trans regions to assist in the recruitment of chromatin enzymes for target genes. In cis, lncRNA
occurs in co–transcriptionally. This suggests that lncRNAs acts as tethers. However, lncRNA are
known to also act in trans when searching for target sites. This determines the importance
chromosomal looping plays in cis effects (Rinn and Chang, 2012). During Archetype IV lncRNA
forms ribonucleoproteins by acting as scaffolds (Kung, Colognori and Lee, 2013). Additionally,
lncRNA in the regulation of gene expression was recent discovered in Xist, a regulatory transcript
found in the X chromosome that mediates the silencing of gene expression (Malecová and Morris,
2010). According to Nagano and Fraser (2011), lncRNA is critical in genomic reprogramming. For
instance, somatic cells that are reconditioned to induced pluripotent stem cells. LncRNA can also act
as a post–transcriptional regulation in Mrna. A lncRNA known as Gomafu/MIAT hinders the
formation of spliceosome and inhibits the splicing of one of the subsets involved in mRNA (Kung,
Colognori and Lee, 2013).
Mediation of lncRNA in gene expression can be concluded to tissue and cell type specifics. In most
aspects it plays a vital

Flipping The Switch : How Cells Use Rna Regulate Genes...
Dr. Tina Henkin's seminar "Flipping the switch: How cells use RNA to regulate genes expression",
was outlined by four general questions. The first question addressed in the seminar was "Why study
Microbes?". The next, "Why study bacterial gene regulation?". The third question, "What are the
basics of gene expression?". Finally, "What's special about riboswitches?". Dr. Henkin addressed
these questions throughout her seminar, which eventually led into to more specific questions of gene
expression and predicted hypotheses of her model. However, to understand these more specific
questions and predictions it is crucial to understand the first four questions outlined in the beginning
of the seminar.
The question "Why study Microbes?", is an ... Show more content on Helpwriting.net ...
In addition, many of the drugs available to treat infectious disease actually originate from bacteria
and fungi. In Biology, constant inquiry of the mechanisms of life lead to new discoveries every day.
Clearly, microbes are very important for studying and understanding our world. Dr. Henkin stressed
their importance in the seminar, specifically the study of bacteria and bacteria's manipulation of
gene expression.
The next two questions, "Why study bacterial gene regulation?" and "What are the basics of gene
expression?" were addressed next in the seminar. Fascinatingly, a bacterial cell knows how to
respond based on their environment. For example, they recognize and respond differently when in
water than in a human. The average bacterial cell has close to 1000 genes, this is significantly more
genetic information that they can use at any given time. These genes are stored in the DNA and each
individual gene provides the information to make an individual product. So, how is a gene
expressed? The first step in this process is called transcription. During transcription, the information
encoded in the DNA is copied by RNA Polymerase to make mRNA. The next step is referred to as
translation. During translation, the information in the mRNA is "translated" to make a protein using
the ribosome. These steps basically turn genes "on and off" in a bacterial cell in response to a
change in their environment. How does this happen? According to Dr. Henkin in her 2008

The Biological And Physiological Mechanisms Of Action,...
Transgenic or Genetically Modified (GM) crops are plants used in agriculture that have been
genetically modified using recombinant DNA technology. The aim for GM plants/crops is to express
a gene or a trait that is not found in the species of the plant. The scientist that modify the plants
insert a foreign gene into the plant's original DNA. As a result to the modification, the plant receives
characteristics within the genetic code. Most, GM plants become resistant to pesticides, however
there are other variables within transgenic crops. Since the genes of humans, plants, and bacteria are
all created from the same genetic material; scientist have a variety of genes to choose from, when
modifying. Within plants, genetic modification occurs in steps . " There are five major steps in the
development of a genetically engineered crop. But for every step, it is very important to know the
biochemical and physiological mechanisms of action, regulation of gene expression, and safety of
the gene and the gene product to be utilized" 1. The first step is mapping; Mapping is locating and
isolating the desired gene before extraction. Once the gene is extracted, it must be cloned. Many
copies are made of the isolated Gene; gene cloning isolates the gene from the entire extracted DNA.
Once it is cloned, the gene of interest is designed and packaged so that it can be controlled and
properly expressed inside the host plant. Polymerase Chain Reaction (PCR) is the cloning process,
and it

Epigenetic Disorders Paper
In the paper "Epigenetic Factors and Autism Spectrum Disorders," epigenetics is defined as the
study of the mechanisms in which genes are silenced or expressed as various phenotypes. Autism
and autism spectrum disorders (ASDs) are considered complex neurodevelopmental disorders. The
article primarily focuses on the etiology and the epigenetic effects that possibly play a role in the
development of the disorders. In the case of monozygotic twins, if one child shows symptoms of
autism, there is a great likelihood both will show symptoms, which proposes a possible genetic link.
However, the diagnosis of autism and ASDs is complex and the symptoms can vary, even for
identical twins. Symptoms of autism and ASDs are also often comparable to symptoms ... Show
UBE3A, GABA receptor genes, and RELN are among some of the genes explored in the article that
are epigenetically regulated and express phenotypes in neurodevelopmental disorders that are
related to autism and ASDs. Epigenetic regulation includes histone modification and both DNA
methylation and DNA demethylation. In histone modification, DNA surrounds the proteins that can
be phosphorylated or acetylated, or likewise, dephosphorylated or deacylated, which can cause the
transcriptional process to be enhanced or prevented. DNA methylation and demethylation can add or
remove a methyl group to a gene causing it to be either expressed or silenced. These effects can
cause a gene to exhibit varying phenotypes. While some neurodevelopmental disorders have a clear
genetic cause, or genetic etiology, autism can have varying phenotypic expression on different
genes, as well as varying levels of expression. This shows that external factors affecting epigenetic
regulation may play a role in how particular genes are expressed. The article also explores the theory
of "intragenomic conflict", and the influences of parent–of–origin genetic inheritance on autism and

Bacteria And Its Effects On The Natural Environment
Microscopic single–celled organisms, such as bacteria, consist of a seemingly simple internal
structure that lacks membrane–bound organelles, yet bacteria thrive in diverse nutritional
environments. The significant ability of bacteria to adapt to a wide variety of nutritional
environments reflects their use of overlapping regulatory systems that link gene expression to
intracellular accumulation of a small number of key metabolites. Bacteria survive using a diverse
array of carbon sources, especially if its main carbon source is absent in their natural environment.
Bacteria have carbon components that we know are required for energy production but how does the
transport of carbon sources, which is in turn utilized in the central metabolic pathway connected to
gene regulation? The central metabolic pathways are those pathways that provide the precursor
metabolites to all the other pathways for the synthesis of macromolecules such as DNA, RNA, and
proteins. Symbiotic interactions between bacteria and its hosts have been studied for about half a
century now to help develop a more detailed view of the reactions that generate the central
metabolites in bacterial cells. In some circumstances, bacteria produce harsh biochemicals as a
response to nutritional stress. The genes that are required for the utilization of nutritional sources are
typically regulated by the availability of the substrate. Similarly, the genes required for the
biosynthesis of particular cellular

Epigenetics Essay
Epigenetics, involves the expression of phenotypical characteristics in an individual without directly
altering the genetic code. Instead the phenotypes manifest through the use of external factors, such
as, trauma, stressors, environment and chemical exposure that result in the silencing and alteration
of gene expression without altering or mutating the genetic code. This essay will look into the
importance of the study of epigenetics through the effects of epigenetics on genes, as well as the
effects of experience and inheritance on the development of epigenetic based phenotypical
characteristics.
The first major effects of epigenetics on genes can be seen in the role of DNA methylation in
mammalian epigenetics. DNA methylation provides a method of gene control in an organism, where
it assures proper gene expression, as well as silencing of genes within cells, it does this through the
manipulation of chromosome architecture, where it affects the packaging of the DNA by the binding
of a methyl group to cytosine (Kullis & Esteller, 2010). The effects of this can ... Show more content
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The expression of these phenotypes and their acquisition can then clearly be seen in the effects of
chemical compounds such as arsenic, nickel and BPA on the development of cancer as well as the
effects of life experiences, such as childhood abuse, on the manifestation of depression. While,
lastly it can be seen how the possible acquisition of epigenetic phenotypes by an individual can
behave similarly to genetic code and be passed through the germ–line to subsequent individuals.
Therefore, this epic influence on survival through epigenetic expression, emphasizes the importance
of the study of

Why Do Genes Make Eukaryotic Cells?
Each cell in our body is composed of the same DNA, yet different cells synthesize different
proteins. In other words, each cell has the same genotype, but different phenotypes. For example,
our pancreatic beta cells make insulin and our epithelial cells make collagen. Why can our
pancreatic beta cells not make collagen and our epithelial cells make insulin? This is all due to gene
expression. Each cell is composed of every single gene, but only a certain collection is expressed.
The regulation of gene expression is more complex in eukaryotes, than prokaryotes. This essay will
discuss both and how key steps and possible decisions influence which cell has which phenotype. In
prokaryotic cells transcription influences what genes are to be expressed. Genes of related function
are grouped together into one transcription unit. This leads to an advantage because a single "on–
off" ... Show more content on Helpwriting.net ...
The first stage is chromatin modification. Usually, genes within heterochromatin are not expressed
since it is so compact and dense. Chemical modifications to histones influence whether the
chromatin is condense or not. For example, histone acetylation promotes transcription by opening
up the chromatin structure. In contrast, DNA methylation reduces transcription by the addition of
methyl groups, leading to condensation. Individual genes as well as long segments of the DNA can
be heavily methylated in cells, preventing them from being expressed. Methylation patters can be
inherited however, unlike mutations, they can be reversed. The next step is regulation of
transcription initiation. Transcription factors can either be specific or general. General transcription
factors are essential for the transcription of all protein coding genes. Specific transcription factors
are specific to the transcription of individual genes. High levels of transcription of particular genes
at the appropriate time and place depend on

Brain Tumor Induced Neurotoxicity Case Study
Brain Tumor Induced Neurotoxicity
Dysregulation of gene expression within the neurons could also result in uncontrolled cell growth
leading to formation of tumors. This was facilitated by expressing the targets of miR–10b–
BCL2L11/Bim, TFAP2C/AP–2γ, CDKN1A/p21, and CDKN2A/p16 that regulated controlled cell
growth. MiR–10b was therefore responsible for uncontrolled cellular growth by downregulating
proapoptotic genes. These miRNAs have been validated to negatively regulate the protein tyrosine
phosphatase μ (PTPμ) gene that has been observed to be down regulated in these tumor cells.
Inhibition of miR–10b decreased growth of the tumor by retraction from the cell cycle and
encouraging programmed cell death. Decreased survival of glioblastoma ... Show more content on
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Morphine functions via the μ opioid receptor to bring about changes in miRNA expression in
neurons. Their chronic use results in undesirable effects such as drug tolerance, opioid–induced
pain, and opioid dependence as well as reducing the size of the dopaminergic neurons [14–15].
Opioid drugs, such as morphine, are a class of powerful analgesics that are used for treating many
forms of acute and chronic pain. This analgesics also forms a common drug of abuse that could have
dire consequences for the neurons upon repeated intake. It is likely that this same mechanism of
toxicity could result in morphine abusers developing symptoms similar to PD patients.
Brain Injury– Induced Neurotoxicity
In an in vitro model of cerebral ischemia, increase of miR–497 expression following oxygen–
glucose deprivation, correlated with increased cell death and down regulation of its anti–apoptotic
proteins, Bcl2 and Bclw [17]. Temporal regulation of miRNA expression has been shown in the
brain of rat models subjected to middle cerebral artery occlusion (MCAo) [20]. An up regulation of
the anti–apoptotic miR–21 has been shown to protect neurons from death in cerebral ischemic
model. The temporal and biphasic regulation of these miRNAs have been proposed to play a crucial
role either in the acute injury phase or the late recovery phase [16]. In addition, biphasic expression
of miRNAs has also been demonstrated in the same animal models. Cerebral ischemia

Mir160-And Mir165 / 66-Regulated Pathways In SE
Importantly for a role of miR160– and miR165/166–regulated pathways in SE, we found that
transgenic forms with defective expression and function of miR160 (miR160b, miR160c, mARF16)
and miR165/166 (STTM165/166) were capable to produce somatic embryos on auxin–free medium
and auxin treatment severely impaired their embryogenic response. Similar capacity for SE
induction on auxin–free medium displayed also the culture overexpressing LEC2 and accumulated
IAA (Ledwoń and Gaj, 2011; Wójcikowska et al. 2013). Similar to the culture overexpressing
LEC2, in embryogenic culture of the miR160 and STTM165/166 we found increased accumulation
of the indolic compounds and enhanced expression of LEC2 that was coupled with activation of the
YUC (YUC1, ... Show more content on Helpwriting.net ...
So far, few TFs directly regulating MIRNA genes have been implicated in plants including
activation of MIR165a and MIR166b by SHR (SHORT ROOT) and SCR (SCARECROW) during
post–embryonic development (Carlsbecker et al. 2010; Miyashima et al. 2013). LEC2 regulation of
MIRNA genes has not been reported yet but it cannot be excluded as FUS3, a TF structurally and
functionally related with LEC2 (Harada, 2001), was suggested to control MIR156, MIR160,
MIR166, MIR396 genes in the embryogenic culture of Arabidopsis (Wang and Perry, 2013).
Altogether, several lines of evidence infer that the miR165/166–PHB/PHV regulatory node controls
induction of the embryogenic program in somatic cells of Arabidopsis through targeting LEC2. The
possible role of miR165/166 in the regulation of HD–ZIP III TFs during SE was also postulated in
sweet orange and Larix leptolepis but the targeted effectors and molecular pathways controlled were
not identified (Wu et al. 2011; Li et al. 2013). Our results suggest that miR165/166–PHB/PHV and
miR160–ARF10/ARF16 regulatory modules might regulate SE induction through LEC2.
Accordingly, the significant changes in LEC2 expression levels in SE cultures with a disturbed
expression and function of the ARF10 and ARF16 genes (mARF16 and arf10arf16) suggest that
these ARFs positively regulate LEC2. In addition, ARF10 and ARF16 seem to contribute to LEC2
regulation in SE

Messenger RNA Interference Pathway
RNA interference pathways play an integral role in the silencing of gene expressions, predominately
by destroying specific targeted molecules of messenger RNA (mRNA). Messenger RNA are single–
stranded RNA molecules which move from the nucleus of the cell to the cytoplasm, while sending
and receiving genetic information from DNA via ribosomes, to where the specific amino acid
sequence of the protein involved in gene expression is located, as the article, "Messenger RNA –
Glossary Entry" explains. The RNA interference pathway (RNAi) breaks double– stranded (dsRNA)
molecules which match a specified targeted gene into short single– stranded RNA (ssRNA), which
triggers the deterioration of the mRNA in its corresponding sequence. According to Cartel, ... Show
It is greatly involved in immunity. Mostly in plants, it is greatly involved in the immune response
system to prevent viruses and harmful genetic material from damaging the cell. In animals, the
RNAi pathway serves an antiviral purpose, providing protection against pathogens, bacteria, and
other harmful organisms that could potentially put the cell in danger. Jaronczyk's findings exaplain
that RNAi pathways also play a large role in the regulation of development of cell growth and
development. It regulates the timing of morphogenesis, a process which organizes the special
distribution of cells during its embryotic development stages. It also regulates the maintenance of
undifferentiated cell types, or those who are not yet specialized. Finally, RNAi pathways help in
RNA activation, and event in which specific short dsRNA molecules bring about the targeted gene
expression. Even evidence of RNA interference pathways are relevant in the everyday lives of
humans such as insecticides, genetically engineered foods, and new treatments for cancer as
described by Hannon in RNAi: A Guide to Gene Silencing

Gene Regulation For Safety Assessment
Gene Regulation for Safety Assessment:
In addition to the mph gene, few gene regulations are implemented as safety assessment for the
product. In the recombination process of making this product, Ecoli plasmid has been used as a
vector to insert mph gene into host bacteria. We use a plasmid vector from E.coli that has conserved
sequence for Plac promoter and gef suicide gene. Plac promoter is positioned upstream of mph gene
to regulate its expression. Later, Plac promoter will be activated by induction with IPTG.
A suicide system in E.coli plasmid vector is used to reduce the potential risk of gene escaping into
the environment. Genetic transfer from GM bacteria to other bacteria via trans–conjugation will
cause unexpected genetic combinations. This method is implemented by using recipient plasmid
with suicide gene gef from E.coli, with expression controlled by Pm promoter. Pm promoter
sequence, which present upstream of the gef suicide gene will control the expression of gef suicide
gene.
The suicide system did not interfere with the performance of the GM bacteria until its physiological
function was activated by specific signal. In developing this product, we use Methyl Benzoate as the
chemical suicide signal. Following the addition of methyl benzoate, the Pm promoter will be
activated, and lead to the activation of gef suicide gene. This activates the suicide system of the cells
and the cell growth will decreases as the cells die.
Plan
Methods:
These procedures

Wnt5a Protein Regulation
WNT5A is a protein encoding gene in chromosome 3p14–p21 which encodes protein WNT5A. The
protein is a member of the WNT family of proteins, and is indicated to activate the planar cell
polarity pathway to induce cell motility and metastasis. (15) In the embryo, the WNT5A pathway
may regulate cell differentiation in morphogenesis as it is expressed in a gradient at the caudal end
of the growing embryo during gastrulation. (16)
The link between up regulation of WNT5A and EMT has been well researched. Increasing
expression of WNT5A shut off several other genes. One of them is KISS–1, a metastasis supressor.
Another example is CD44, tumor cell homeing and metastasis antigen. Some other genes will be up
regulated by WNT5A. This includes gene vimentin, ... Show more content on Helpwriting.net ...
Such drugs are known as PKC inhibitors. This includes staurosporine, a microbial alkaloid and
precursor to many novel PKC inhibitors which compete at PKC's ATP binding site. Newer drugds
like N–benzoyl–staurosporin and –hydroxystauro–sporin improve selectivity and demonstrated
better therapeutic effect in vivo. (21) The problem for existing PKC inhibitors is that they are
relatively non–selective in their actions. In the future better drugs can be developed if they target
specific isozymes in order to differentially inhibit PKC functions. (21) Some other researchers study
the down stream products of PKC pathway, like vimentin, as a anti–cancer therapeutic target. For
example, withaferin–A increases apoptosis and vimentin cleavage in vimentin expressing tumor
cells and it has been proved that this drug has pronounced anti–antiogenic effect with little adverse
effect in non–proliferating endothelial cells. (22) It also significantly blocks soft tissue sarcoma
growth and

Teloomerase Research Paper
Telomerase (TERT) is an enzyme responsible for maintaining the ends of telomeres and reversing
the process of telomere shortening in humans by adding a "TTAGGG" polynucleotide to the 3' end
of the telomere. The addition of the "TTAGGG" compensates for inefficiencies in replication of the
ends of DNA in eukaryotes. Telomerase is limited to highly proliferative cells such as germ cells and
lymphocytes where the telomerase is necessary to maintain telomere length, and the telomeres
themselves are not sufficiently long to facilitate such rapid cell division without incurring damage to
the DNA. Most somatic cells exhibit no telomerase activity and in cells where telomerase is present
telomerase activity is strictly regulated. In cells that exhibit

Vibrio Ficheri Case Study
the DNA. Binding of the regulatory protein activates transcription which results in the production of
mRNA product which is then translated to protein product.
Type III secretion systems are needle like proteins that span the inner and outer membrane in gram–
negative bacteria. Gram–negative bacteria with T3SS use the needle to penetrate other bacteria, and
then secrete proteins from their bacterial cytoplasm into the cytoplasm of the host.
b. What might this regulatory system look like (use Vibrio fischeri as a model; 6 pts)?
Vibrio fischeri uses quorum sensing to determine when cell density is sufficient to produce light.
Light from a single bacterium is not useful so it is more beneficial for many bacteria to luminesce
together. Bioluminesence

Mitochondria and Chloroplasts Descended from Free-living...
Mitochondria (mt) provide critical function in (a) maintenance of cellular energy supplies, i.e.,
thermoregulation and synthesis of essential molecules (such as phospholipids and heme); (b)
apoptosis or programmed cell death; and (c) mediating multiple cellular signaling pathways (Ryan
and Hoogenraad 2007). It is widely accepted that mitochondria and chloroplasts descended from
free–living bacterial ancestors (Dyall et al. 2004). Following their acquisition by eukaryotic cells
during endosymbiotic evolution, most of the genes in these organelles were either lost or transferred
to the nucleus. Today, it is demonstrated that from all mitochondrial proteins (over 1500) most of
them (93–99%) are encoded in the nucleus, synthesized in the cytoplasm and then imported into the
organelles (Woodson and Chory 2008). For instance, human mtDNA only contains 37 genes and
codes for 13 encoding polypeptides, 22 tRNAa, and 2 rRNAs (Ryan and Hoogenraad 2007). The
relationship between organelles and the nucleus is continually evolving to suit an organism's needs.
Based on the above–mentioned close relationship, a strict communication between mitochondria,
chloroplasts and the nucleus is indispensible. Hundreds of genetic diseases in humans and thousands
of phenotypic variations in plants and other organisms are known to be the result of alterations
affecting nuclear–mitochondrial (NM) communication. These communication mechanisms include
both nucleus to organelle (antrograde) and organelle

Gene Expression : The Consequences Of Human DNAAnd Human...
Human DNA is found in 23 pairs of chromosomes and within these chromosomes are sections of
DNA called genes. Genes make up the physical traits inherited and expressed from mom and dad.
When the DNA found within these genes provides genetic instructions to encode proteins or other
molecules, this is called gene expression. Gene expression is the process by which genetic
information stored in a gene dictates a cells function. This process is essential as regulatory proteins
control the rate of gene expression. Gene expression is influenced by the processes performed in
transcription and translation to make functional proteins. The regulation of gene expression is more
complex in Eukaryotic cells then prokaryotic cells due to the nuclear ... Show more content on
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Gene expression can be altered by different genetic and epigenetic mechanisms. These mechanisms
can alter chromatin structures and the accessibility of DNA, thereby regulating patterns of gene
expression (Wajed, S. A., Laird, P. W., & DeMeester, T. R. 2001). In the nucleus of the cell,
chromatin is bound to a DNA–histone–protein complex in the form of chromosomes. Within the
cell, chromatin modifications are made such as DNA methylation and histone modification in order
to alter gene expressions. DNA Methylation involves the addition of a methyl group to the 5' end of
the cytosine ring within CpG dinucleotides. While most CpG dinucleotides are methylated,
unmethylated CpGs are clustered together at promoter regions of many genes (Lim, D. H., & Maher,
E. R. 2011). These promoter regions are essential for transcription to occur, however, DNA
methylation can prevent transcription factors from binding leading to changes in chromatin
structures. Another mechanism that can alter gene expression is histone modifications. Histone
modification includes changing the composition of histones or the addition of acetyl, methyl or
phosphate groups onto the amino acids of histone tails (Book). While histones are important
proteins used to organize and wrap large amounts of DNA, when histones within these nucleosomes
are modified, the mobility and positioning of DNA are affected resulting in gene promoters to be
activated or repressed. In addition to both of

Essay On Sequence Processing, Alignment, And Transcripts...
2. Sequence processing, alignment, and transcripts assembly To get high–quality clean reads, the
assessment of sequencing quality and read processing were performed by fastQC
(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FASTX–Toolkit
(http://hannonlab.cshl.edu/fastx_toolkit/). The low–quality reads were removed using the same
filtering criteria as described previously []. The clean reads were aligned on the F. vesca reference
genome [1] using HISAT2 using default parameters [2]. Stringtie with higher accuracy and precision
was used to generate transcript assembly [2]. Meanwhile, all unmapped reads derived from the
above libraries were de novo assembled using the Trinity under default parameters to obtain
comprehensive ... Show more content on Helpwriting.net ...
The remaining transcripts filtered by above filtration steps were considered as putative lncRNAs. To
understand the biological function of lncRNAs, the target genes were predicted based on cis–acting
and trans–acting modes [6]. The sliding window strategy was used to search cis–acting target genes
within 10 kb upstream and downstream of lncRNAs []. To identify lncRNAs that may act in the
trans–acting mode, the expression correlations between lncRNAs and all genes were calculated. The
above analysis was performed using the perl and R scripts. 4. Functional annotation of protein
coding transcripts The protein coding transcripts were compared with sequences in Nr protein and
nucleotide (Nt) databases, the Swiss–Prot protein database to assign potential function onto
transcripts. The program Blast2GO [7] and InterproScan [8] were used to obtain GO annotation of
the transcripts and identify protein domains, respectively. GO and enrichment analyses were
performed using GOseq, involving biological process, molecular function, and cellular component.
The metabolic pathways were predicted using KAAS [9], and KOBAS 3.0 [10]was used to test the
statistical enrichment of differentially expressed lncRNA target genes. Complementarily, genome–
wide prediction of the

Essay On Circrna
Despite several sporadic reports about the identification and potentially biological functions of
circRNAs in reproductive organs, the research regarding the functional roles of circRNAs in this
field still is at its infancy. However, these early stage studies shed light for further investigation. The
current reports of circRNAs in the reproduction system are summarized in the Table 1.
The expression of circRNAs in oocyte and pre–implantation embryo development
Some investigations have indicated that numerous genes, including non–coding genes, are engaged
in the regulation of oocyte and embryo development [72, 73]. The expression pattern of some genes
can be used as potential biomarkers. Since circRNAs are extensively involved in the ... Show more
content on Helpwriting.net ...
A novel single–cell universal poly (A)–independent RNA sequencing (SUPeR–seq) technology has
been used for deep sequencing of mouse pre–implantation embryos [76]. A total of 2,891 circRNAs
from 1,316 host genes were detected in mouse oocytes and early embryos (from zygotes to
blastocysts). Most circRNAs, with a length of less than 2kb, are derived from internal exons in the
same host gene. Moreover, about 91% of circRNAs consist of multiple exons [76]. Different from
what has been reported in amphibian [74], the expression pattern of these circRNAs shows a
typically developmental stage–specific feature. Additionally, the gene ontology analytical data of the
host genes producing these circRNAs srevealed that the circRNAs presented in early embryos of
mice are potentially responsible for chromosome organization, cell division, and DNA repair [76].
The same group further analyzed the number of circRNAs at each embryonic stage. Approximately
2,278 circRNAs were presented in metaphase II (MII) mouse oocytes. After fertilization, the
circRNA number in zygotes sharply reduced to 1,850. At the four–cell embryo stage, the lowest
number of circRNA was found to be only 1,422. However, at the morulae stage, the circRNA
number increased to 2,799. Again, the circRNA number strikingly decreased to only 779 in the
blastocyst stage, suggesting the existence of a degradation mechanism of circRNAs during the
morulae–to–blastocyst transition [76]. The fluctuation of circRNA

Role Of Ncrna
The central dogma of biology holds that genetic information generally results from DNA to RNA to
protein., this directional view has been changed by the emergence of non–coding RNAs(ncRNA) in
gene expression. ncRNA is small RNA that constitute a large family of RNA that do not code for
protein formerly seen as a waste, but that does not mean that these RNA does not have a biological
function. Most importantly, they are shown to be implicated in the regulation of transcription and
post–transcription mechanism in gene expression. Some the regulatory ncRNA include
microRNAs(miRNA), circular RNAs(circRNAs), and long non–coding RNAs (IncRNAs). This
review summarizes the mechanisms and examples where these ncRNAs regulate transcription and ...
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A single pri–miRNA often contains sequences for several different miRNAs. Pri–miRNAs fold into
hairpin structures containing imperfectly base–paired stems and are processed in two steps,
catalyzed by the RNase III type endonucleases Drosha and Dicer. Both Drosha and Dicer function in
complexes with proteins containing dsRNA–binding domains (dsRBDs). The Drosha–DGCR8
complex processes pri–miRNAs to ∼70–nucleotide hairpins known as pre–miRNAs. In animals,
pre–miRNAs are transported to the cytoplasm by exportin5, where they are cleaved by Dicer
(complexed with TAR RNA binding protein (TRBP) in mammals to yield ∼20–bp miRNA
duplexes. One strand is then selected to function as a mature miRNA, while the other strand is
degraded. Occasionally, both arms of the pre–miRNA hairpin give rise to mature miRNA.
The miRNAs control gene expression post–transcription through different mechanisms such as
repression at the initiation step by repression by preventing 60S subunit joining, deadenylating,
proteolysis, and slow elongation or ribosome drop–off. This mechanism regulates mRNA translation
or stability in the cytoplasm via non–perfect pairing with target mRNAs. Usually involving a seed
pairing of just six to eight nucleotides in length cause degradation of target RNAs by the RISC
complex in the case of perfect complementarity with the target site–the phenomenon known as
RNAi. It is estimated that approximately one–third of human protein–coding genes are controlled by
miRNA.

Factors That Regulate Expression Of Stress Responsive...
Science I Term Paper
The research paper that this term paper is based on is Interactions Among Plant Transcription
Factors Regulating Expression of Stress–responsive Genes, Sony Malhotra and R. Sowdhamini,
National Center for Biological Sciences, June 2014, Bioinformatics and Biology Insights.
Abstract:
Plants are known to respond to abiotic stress by up or down regulating their genes. This is done by
activating transcription factors. It is known that these transcription factors, though they have DNA–
binding domains, interact amongst each other for the regulation of gene production. In order to find
out which transcription factors interact and how, the research uses genetic and molecular structure
information available in databases and computationally analyses the data. The factors that lead to the
conclusion of interaction between transcription factors includes spatial proximity and possible
interaction poses. Molecular docking is used to predict the interaction poses and DockScore is a
scoring system used to rank the interaction poses.
Introduction:
Plants are immobile and therefore need mechanisms to counteract stresses that they face from their
environment. Cold, high light, drought, salinity, abscisic acid, rehydration and combination of
stresses like cold–drought–salt stress are common abiotic stresses that plants encounter. In order to
deal with these stresses, plants either up regulate or down regulate their genes; that is, they increase
the production of

taking a Look at MicroRNAs
MicroRNAs (miRNAs) are evolutionary conserved small (21–23 nucleotide long) non–coding RNA
molecules that are involved in post–transcriptional regulation of gene expression. The human
genome encodes for upward of 500 miRNAs and each can usually regulate a whole set of genes
involved in various kinds of molecular mechanisms although a lot of mRNA targets of individual
miRNAs are still not known. miRNAs are involved in regulation of crucial functions related to cell
growth, development and differentiation and have already been linked with various diseases like
cancer, heart disease etc. miRNAs can be encoded by their own genes or can sometimes be found in
the introns of the genes they regulate thus undergoing the same transcriptional regulation. After
transcription they are folded, processed and exported from the nucleus as a precursor dsRNA. In the
cytoplasm they bind the Dicer endonuclease that cuts the RNA into short segments of approximately
21 nucleotides, which then bind the Argonaut protein where one strand is selected and remains
bound to the protein and the other one is degraded. The guide strand together with the Argonaut and
other proteins form the RNA Induced Silencing Complex (RISC). Through base complementarity
between the guide strand and the mRNA, the complex can either inhibit translation or catalyze
cleavage of the mRNA after which it is degraded. Unlike siRNAs that have perfect complementarity
with the mRNA, the miRNAs have a partial complementarity with a

A Note On Cellulose
Gene expression
Fatty Acid metabolism
(Graphs will be added)
Hepatic gene expression profiles of genes primarily associated with fatty acid metabolism for rats
fed cellulose (control) diet, FOS, β–glucan and pectin. Results represent the mean fold change (SE)
compared to control and presented as means ± SD, n = 9–10 per group.
With respect to fatty acid binding proteins, Fabp2 have shown down–regulation in all of the diet
groups compared to the cellulose (control) group (P = 0.002). (fig 6 –1) Conversely, there was a 0.5
fold down–regulation of Fabp5 in all the fibre group compared to the cellulose (control) group (P <
0·001) (fig 6–2). While, there was a 1.2–fold up–regulation of Fabp3 in the Pectin fibre group
compared to the ... Show more content on Helpwriting.net ...
(fig 7–2)
On the other hand, HMGCS1 showed 1–fold down–regulation in FOS group (P = 0.018) compared
to the cellulose (control) group, while in the β–glucan group (P = 0.121) group and pectin (P =
0.312) there was no statistically significant difference compared to the cellulose (control) group (fig
7–3). While, Scd1 have shown down–regulation in FOS group (P = 0.003), β–glucan group (P =
0.0018) and pectin group (P = 0.001) compared to the cellulose (control) group (fig 7–4). CRAT
have shown up–regulation in pectin group (P = 0.005) compared to the cellulose (control) group, on
the other hand, there was no statistically sigmificant difference between FOS group (P = 0.54) and
β–glucan group (P = 0.25) compared to the cellulose (control) group (fig 7–5). While, ACAT have
shown up–regulation in pectin group (P = 0.024) compared to the cellulose (control) group, on the
other hand, there was no statistically significant difference between FOS group (P = 0.23) and β–
glucan group compared to the cellulose (control) group (P = 0.181) (fig 7–5). Acadl have shown
down–regulation in FOS group (P = 0.001), β–glucan group (P = 0.001) and pectin group (P =
0.007) compared to the cellulose (control) group (fig 7–4).
Cholesterol metabolism

Epigenetic Modifications
INTRODUCTION
Epigenetic mechanisms such as DNA methylation and histone modifications are widely considered
to be important in controlling the differentiation of cells. However some argue that since these
mechanisms are not seen or transient in model organisms such as worms and flies that epigenetics
cannot be important. However it is also important to mention that there are very different definitions
of the word epigenetics formed from independent reasoning which may affect the debate on whether
epigenetics is important or not in controlling cell differentiation. (Berger et al., 2009)For example,
to Conrad Waddington, it was the study of epigenesist ie. How genotypes give rise to phenotypes
during development. On the other hand, Arthur Riggs ... Show more content on Helpwriting.net ...
In the first cell division these transcription factors are distributed asymmetrically to the daughter
cells. Then, and in subsequent cell generations, new patterns of gene expression arise in two ways:
as a matter of course (some transcription factors activating expression of genes encoding other
regulatory proteins, etc.), and in response to signals sent by other cells. Signalling used in
development affects expression of genes encoding yet more transcription factors–it does so by
changing activities of transcription factors, already present, which target those genes. Retinoic acid
and growth hormone are examples of such signalling molecules. (Ptashne, 2013)
There are two things we need to keep in mind when we talk about cell differentiation. These are
specificity and memory. Transcription regulators work specifically. They activate one gene or set of
genes and not another. Therefore, for many regulators and genes, any regulator will work on any
gene as determined by the locations of its affined cis–regulatory sequence. (Ptashne,

Gene Expression Lab Report
Through multiple experiments, promoter elements were examined to see how they control gene
expression. The purpose was to learn how a gene is regulated in bacteria, how timing affects
activity, how positive and negative regulation control gene expression, how E. coli mutants respond
in plate assays, and how concentrations of sucrose affects gene expression. ß–galactosidase enzyme,
also known as Beta–gal or ß–gal, was the assay in the experiments. ß–galactosidase is an enzyme
that breaks up lactose into galactose and glucose. Furthermore, it is a hydrolase enzyme that
catalyzes the hydrolysis of ß–galactosides into monosaccharides.
E. coli is often used in biology labs and is easy to manipulate. "E. coli are rod shaped bacteria that
are found ... Show more content on Helpwriting.net ...
Once lab began, the IPTG was added to the time 0 samples cultures, a final concentration of 1mM
was added to both cultures, and the timer was started. Every 30 minutes over a time period of 90
minutes 2ml was removed from each culture and the initial flask was returned to the 37°
environment to continue growing. The 2ml was equally divided into two different test tubes. The
tubes were labeled A and B. There was four tubes at each time point; 2 for lacZ+ and 2 for lacZ–.
Tube A was the control tube, which contained .2ml of water. Tube B was the experimental tube,
which contained .2ml of water and .013M ONPG. The tubes were then incubated in 37° bath water
for 20 minutes. After 20 minutes elapsed the tubes were removed and 2.7ml of 1M Na2CO3 was
added to each tube. Next 1ml was transferred from each tube into a cuvette, which was placed in the
spectrophotometer at 420nm. A spectrophotometer, also known as a spec, reads the intensity of light
(absorbance level of liquids). Tube A was inserted first in order to blank the spec, and tube B was
second, so we could record the absorbance of the solution. The absorbance was recorded for each
cuvette containing a solution from tube B. The A420 recordings we were needed to determine ONP
produced in mmol and the activity. The formula for activity is ONP produced divided

Essay on The Unhealthy Focus on Competition in Universities
The first thing I do when I wake up in the morning is secure my knapsack, ensuring that my rations
are in their proper place: my biology textbook, notebook, and iclicker2. Then, I begin my long
march into enemy territory. My blitzkrieg strategy will help me win this war. My ground attack is
relentless (hand cramping but pen scribbling down the highlights of the facts about a prokaryotic
cell's genome). My aerial assaults, though few, are aggressive and well timed (Dr. Newman,
question, if we remove the repressor gene, will the lac operon...). And all the while, I cleverly evade
the snipers, positioned strategically by the enemy in the back of the room. They fire at me with
deadly accuracy (iclickers ready to answer the lecture ... Show more content on Helpwriting.net ...
Every facet of our life revolves around our seemingly insatiable appetite for competition. We teach
our children (as we were convinced long ago) that their peers are not resources and friends to learn
from, but enemies to overcome, to beat. We grow up, convinced that self worth is dependent on our
record of triumphs. We apply to colleges, happy when our top choice school accepts us but elated
when the same isn't true for our neighbors. Even applicants who are not competing for positions
against each other compete. Imagine your Pitt acceptance letter juxtaposed with a friend's – no,
competitor's – Ivy League letter. (You lost this round.) We work for businesses, which compete for
the majority share of the widget market. As employees, we compete for bonuses, promotions,
vacation time, etc. (Lets not forget the cheery "Employee of the Month" Award, given only to the
most friendly and courteous of all staff. Now even social interactions are competitive.) For fun, we
play games that strictly mandate a winner and a loser. We recite the tired, worn–out mantra:
competition builds character, which only serves to fulfill our desire to categorize each other.
Nothing can escape our gluttonous lust for external validation. Want to go out with friends? Who
can drink the most shots? Having luncheon with Doris and Eugene? Whose grandchildren are more
successful? Going to class? Who was smart enough to get question 45 right on the last exam? Even
sibling rivalry,

A Short Note On Gene Regulation And Expression
BS31006 – Gene Regulation & Expression – Dr. Armel Nicolas
Genome engineering using the CRISPR–Cas9 system
Matei Agavriloaei – 120004682
24/11/2014
ABSTRACT:
Modified nucleases have been used for years in order to achieve successful genome editing and are
nowadays an almost universally–used method. RNA–guided nucleases (such as Cas9) with easily
changeable characteristics have been generated in great numbers especially since the emergence of
clustered regularly interspaced short palindromic repeats (CRISPR). This represents the most
modern tool that can be used by scientists for genome editing. This technology can bring a broad
range of medical benefits and advancements (1).
CRISPR–Cas systems:
CRISPRs are DNA loci that include ... Show more content on Helpwriting.net ...
Figure 1: Overview of the CRISPR–Cas system – it shows the adaptive immunity with the use of
viral DNA (3);
Cas genes code for proteins related to CRISPRs. This association is a prokaryotic immune system.
CRISPR spacers recognize and cut the foreign DNA material, just as RNAi does in eukaryotic
organisms (2).
In 2013, this system started being used (and is still widely used today) for adding and changing
sequences of targeted genes (4), process also known as genome editing. The genome can be cut any
location by guiding properly RNAs into a cell and also delivering Cas9 protein. In theory, it could
be possible to build RNA–guided gene drives with the use of CRISPR to alter the genetic code of
entire populations (5).
CRISPR–RNA (crRNA) and Cas proteins come together and form CRISPR–ribonucleic proteins
(crRNPs) for appropriate targeting and cleaving of the foreign nucleic acid (3).
Due to the accelerate evolution of the immune system, the CRISPR–Cas systems are highly diverse
and have been catalogued into three main types, each of them having a specific Cas protein. Type I
and III and related and contain Cas3 nuclease–helicase and Cas10 (a protein with an unknown

function) respectively. Type II is phylogenetically different and is represented by the Cas9 nuclease.
Type II has three different subunits (A, B and C) and their crRNPs are all known as Cas9
complexes. They are restricted only to bacteria, not being in present in archaea as well (3).

Gastrointestinal Tract Research Paper
Abstract After entering the gastrointestinal tract on the way to their physiological site of infection,
enteric bacteria encounter a remarkable diversity in environmental conditions. There are gross
differences in the physico–chemical parameters in different sections of the Gastrointestinal tract
(GI) tract e.g. between the stomach, small intestine and large intestine. Furthermore, even within a
certain anatomical site, there are subtle differences in the microenvironment e.g. between the lumen,
mucous layer and epithelial surface. Enteric pathogens must not only survive passage through the
rapidly changing environments encountered at different niches of the GI tract but must also
appropriately coordinate expression of virulence determinants ... Show more content on
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Several studies have revealed pathogen specific responses to bile that alter the expression of
virulence factors. When V. cholerae was grown in the presence of bile, expression of the essential
virulence genes ctxAB and tcpA was drastically repressed [30]. Since bile is a heterogeneous
mixture, crude bile was fractionated, and the components that mediate virulence gene repression
were identified. It was shown that unsaturated fatty acids (UFAs) present in bile, arachidonic,
linoleic, and oleic acids were responsible for repression of ctxAB and tcpA genes [31]. However,
expression of toxT encoding the direct transcriptional activator of ctxAB and tcpA was not affected
and ToxT protein levels were similar between V. cholerae grown in the presence or absence of bile
or UFAs [31]. Subsequently, the crystal structure of ToxT revealed that unsaturated fatty acids can
bind to ToxT and keeps ToxT in a 'closed' conformation that is not capable of binding DNA [32].
Hence ToxT cannot activate expression of ctxAB and tcpA in the presence of bile or UFAs and the
genes continue to be repressed by H–NS [33]. Bile also causes drastic repression of virulence genes
in salmonellae. Salmonellae grown in the presence of bile demonstrated a marked

Functions Of The Mechanism Of Gene Expression
Researchers daily utilize the knowledge of the mechanism of gene expression, allowing them to
operate in different areas. An example is the imposition of certain conditions to micro–organisms,
which are capable of producing drugs or induce cells to function properly, which is of great
importance in medicine. Great emphasis is placed on control systems based on proteins but recently
research started to also focus on the use of systems based on RNA, which is equally as polypeptides
involved in the regulation of processes such as transcription, mRNA degradation and translation.
Ribonucleic acid can regulate gene expression by the presence of the particles in the chain, where
the individual parts are complementary to each other and can form hydrogen bonds therebetween to
form a secondary structures. TRANSCRIPTION transcriptionis the first stage of gene expression. Its
mechanism is based on rewriting the genetic information contained in the nucleotide sequence of the
DNA strand to the RNA. The process can be divided into the initiation, elongation and termination.
In a first step, an RNA polymerase binds to the denatured template locally at the site promoter.
Then, in elongation step, it adds more ribonucleotides, complementay to the DNA strand, to the
nascent mRNA in the 5 '→ 3 '. The process terminates at terminacyjnym, which mostly is
characterized by regions complementary to each other, resulting in the formation of secondary
structure in a transcript hairpin [5]. In

Andrew Fire And The Biological Sciences
Andrew Fire's Contribution to the Biological Sciences The Earth is full of complex organisms, each
with specific adaptations and behavior patterns that help them thrive in their environment. In order
to grow and develop into these specialized beings, something profoundly important exists at the
genetic level: gene regulation. Gene regulation is the process by which living organisms alter the
frequency or expression of specific portions of their DNA, occurring through many different
mechanisms. This sort of genetic policing helps living creatures to coordinate specific responses to
their environment, or stimulate growth and development in the most efficient manner possible. In
the 1990's, scientists thought that they had a comprehensive understanding of a multitude of
regulatory mechanisms, until biologist Andrew Fire published his research outlining a previously
unknown process: RNA interference. Andrew Fire was born in the San Francisco Bay Area on April
27, 1959. After spending his formative years in the surrounding area, he studied at the University of
California, Berkeley where he spent his undergraduate career studying mathematics. Upon
completion of his bachelor's degree in 1978, he was accepted into the Massachusetts Institute of
Technology for a graduate biology program (BRITTANICA). During his years at MIT, he worked
with biologist Philip Sharp studying introns, for which Sharp was consequently awarded the Nobel
Prize for Physiology or Medicine. Fire finished his

Negative Regulation Of Sheepmeat Odour And Biogen ( SEPW1 )
For the SNP g.53617063 G>A mutation in the present study, quantitative realtime–polymerase chain
reaction (qRT–PCR) analysis revealed that individuals with AA genotype expressed lower mRNA
levels than those with AG and GG genotype. But it requires further investigation to determine
whether this difference is also associated with mRNA stability. It is widely accepted that SEPW1 is
a negative regulator of sheepmeat odour and flavour, and decreased SEPW1 mRNA expression
levels could cause lower odour and flavour. From these results, we can postulate that the SEPW1
gene is negatively associated with odour and flavour, or that the sepw1 gene may affect fatty acid
(FA) metabolism and f the triglyceride (Kubiak et al 2016). The mRNA ... Show more content on
Helpwriting.net ...
SelW expression it has been found to work as regulated during C2C12 cell differentiation (Noh et al
2010). The mRNA level of SelW through the differentiation process of myoblasts and the optimal Se
concentrations for expression of SelW mRNA in chicken myoblasts is 10−7 M is influenced by Se(
Ruan et al 2012.) Overexpression of SEPW could decrease the H2O2– influence oxidative
damage.furthermore, the increased expression of certain antioxidative selenoproteins could regulate
oxidation–reduction homeostasis in cells, improve the ability of cells to save against oxidative stress
and reduce the oxidative damage and the concentration of H2O2 (Yao et al 2014). overexpression of
SelW experiment indicated that it might play important role in component of the cellular defense
system against oxidative stress (Sun et al., 2001) . Increased of Malondialdehyde (MDA) levels
found to be induced with SEPW1 deficiency , also It is reported that Sepw1 deficiency reduced the
ability of myoblasts to buffer the exogenous H2O2 and increased the sensitivity of cells to H2O2.
Therefore, Sepw1 plays beneficial role in antioxidative functions in myoblasts also indicating that
Sepw1 and Gpx1 may play important roles in the response to oxidative stress in chicken myoblasts.
Therefore, chicken Sepw1 also preserves antioxidative function (Yao et al 2014).
Selenoprotein deficiency conducted to thereby suppressed T cell proliferation in response to T cell
receptor

Ho-1 Essay
Although MAPK's play a pivotal role in the induction of HO–1 in response to diverse stimuli, some
other signaling molecules/pathways also mediate HO–1 expression. PI3K Mounting evidence
suggests that the PI3K/Akt signaling pathway mediates the activation of HO–1. Besides, it might be
intimately coupled with the beneficial effects of HO–1 [49]. For instance, expression of HO–1 was
diminished in human lymphocytes with the inhibition of PI3K by15d–PGJ2 [50]. It has been
reported that STAT–3 and PI–3K pathways are required for the up–regulation of HO–1 by IL–10
[51]. Moreover, an increase in ho–1 gene expression was observed in dopaminergic neuronal cells
through the stimulation of PI3K/Akt by nerve growth factor and hemin [52]. PI3K/Akt has ... Show
NF–kB mediates HO–1 response to diverse stimuli has been shown to be activated by insulin in
mammalian cells [55]. Some studies suggest functional binding sites for NF–κB on the promoters of
the rat and mouse HO–1 genes. In the proximal rat HO–1 promoter region a κB element has been
observed to control HO–1 induction by the phorbol ester phorbol myrisate acetate (PMA).
Furthermore, HO–1 was not induced in response to PMA in mice deficient for the NF–κB subunit
p65 and was mediated via an I–κB–kinase–independent pathway [56]. Li and colleagues have also
observed a functional κB element in the mouse HO–1 promoter. They have reported the
involvement of p50 and p65 subunits of NF–κB as well as the inducible NO–synthase in the up–
regulation of HO–1 in vivo [57]. AP–1 AP–1 may play a crucial role for the induction of the mouse
HO–1 gene. Subsequently, various functional AP–1 sites, which mediated inducer–dependent gene
expression of HO–1, have been identified in the promoter regions of the rat and human HO–1 genes
[58]. However, elucidation of the molecular mechanisms involved in AP–1 dependent HO–1 gene
up–regulation has faced some challenges. First AP–1 binding sites in the HO–1 promoter mediate
HO–1 gene expression through the synergistic association of AP–1 with other transcription factors
like USF2, SP–1 etc in various cell culture models [59], [60]. Secondly, the AP–1 site is contained
in the consensus

Examples Of Epigenetics

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Examples Of Epigenetics