H2A Case Study

H2A Case Study
Also, a recent study of an H2A.Z/H2A nucleosome structure shows that the H2A.Z L1 loop domain
was drastically altered without any structural changes of the H2A L1 loop, thus avoiding steric
clash. So, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z
nucleosome (H2A.Z/H2A.Z) (Horikoshi, Arimura et al. 2016). Consequently, the presence of H2A
versus H2A.Z in the histone octamer affects the stability of the nucleosome (Coleman–Derr &
Zilberman, 2012b; Jin & Felsenfeld, 2007; Jin et al., 2009; Kumar & Wigge, 2010).
Since its identification, H2A.Z has been extensively studied in yeast, animals and plants. These
studies have revealed many contradictory roles of H2A.Z in modulating chromatin dynamics and
transcription ... Show more content on Helpwriting.net ...
8A) (Coleman–Derr & Zilberman, 2012a; Sura et al., 2017; Zilberman et al., 2008). At highly
expressed protein coding genes, H2A.Z is intensely enriched around the nucleosome–depleted
region (NDR) at transcriptional start sites (TSSs), particularly at the +1 nucleosome (i.e. the first
nucleosome downstream of the TSS) (Coleman–Derr & Zilberman, 2012a; Sura et al., 2017; Zhang
et al., 2016; Zilberman et al., 2008) (Figure 8B). The +1 nucleosome can act as a barrier to
transcriptional elongation by blocking and stalling RNA Polymerase II (Nock et al., 2012; Weber et
al., 2014). H2A.Z incorporation moderates the nucleosomal barriers to RNA Polymerase II
progression, likely by facilitating the loss
31
of an H2A.Z/H2B dimer from nucleosomes when encountered by RNA Polymerase II (Weber et al.,
2014). Therefore, accumulation of H2A.Z around TSSs promotes transcriptional initiation. In
Arabidopsis, H2A.Z is required for activation of Flowering Locus C (FLC), in that way ensuring the
proper timing of the transition from vegetative growth to flowering (Deal et al., 2007). It is shown
that the TSS of FLC locus is enriched with H2A.Z and its expression is strongly up–regulated by
FRIGIDA (FRI). FRI acts as a scaffold protein in a transcription activator complex that binds to the
FLC locus and directly associates with the SWR1 complex, suggesting that FLC up–regulation is
mediated by direct modulation of H2A.Z deposition by FRI (Choi et al., 2011).
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Gel Arabidopsis Case Study
RESULTS Agarose GE: Figure 1 shows the results of amplifying five types Arabidopsis thaliana
fwa gene. successful PCR was a result of nice bands showing in figure 1. Wild type undigested
(900bp), mutant undigested(860bp), and mutant digested (850bp) were all showing band in the same
location. On the other hand, Wild type digested did not show any bands meaning amplification did
not occur because McrBc digests fwa enzyme that is being methylated. Gel electrophoresis was used
to determine the size of the base pairs from the logarithmic equation. Digested and undigested
mutant genes showed hazy regions meaning they have less amount of amplification compared to
wild type undigested which shows a significant amplification. No band was shown for

Significance Of Histone 3 Gene Family In Arabidopsis Thaliana
It is fascinating to know that two meters of human DNA are packed inside ∼1000 µm3 nucleus.
How this amazing packing occurs in nature was a great mystery until the discovery of nucleosome
and its structural organizations. Nucleosome is a basic unit of chromatin that consists of 146 bp
fragment of DNA wrapped around a protein octamer known as histone. One nucleosome contains
two molecules of each Histone 2A, Histone 2B, Histone 3 and Histone 4. Besides that, Histone 1 is
linked with DNA that connects various histones in the nucleosome (Kamakaka and Biggins, 2005).
All these histone proteins belong to different gene families but this review will focus on histone 3
gene family in Arabidopsis thaliana.
Histone 3 gene family
The number of ... Show more content on Helpwriting.net ...
Histone3.3 impacts plant development and transcription
H3.3 is encoded by three HISTONE 3 RELATED (HTR) genes, HTR4 (At4g40030), HTR5
(At4g40040), and HTR8 (At5g10980), which are expressed in all tissues throughout the
developmental stages (Okada et al., 2005). Wollmann and colleagues studied function of the H3.3 in
Arabidopsis by utilizing mutant lines (Wollmann et al., 2017). Since single and double mutant of
H3.3 subfamily did not have phenotype, triple mutant was used for the study. h3.3 kd–1 and h3.3
kd–3 plants were smaller than wild type and had serrated leaf margin and decreased fertility (Figure
2). H3.3 knockdown caused a variety of pleiotropic effects in plants possibly by changing the
transcription. Thus, the impact of H3.3 knockdown on transcription was studied by using RNA–seq
analysis. More than 900 genes were significantly mis–regulated in h3.3kd with the majority being
downregulated (Figure. 2). Gene ontology term analysis (GO–Term) of downregulated genes
revealed a large variety of response processes, including environmental and endogenous stimuli.
Wollmann and colleague demonstrated that H3.3 is not required for gene expression in a global
scale but the loss of H3.3 directly or indirectly affects the expression of genes related to response to
internal and external stimuli.
H3.1 binds to silent genes and H3.3 binds to active genes
To determine the genome wide binding of H3.1 and H3.3 proteins, Chromatin

Plant Arabidopsis Thaliana Summary
Summary
Dr. Alice Cheung studies the molecular mechanisms behind mating in the plant Arabidopsis
thaliana. The male pollen tube is lured toward the female ovule, which leads to bursting of the
pollen tube and the release of cytoplasmic sperm, permitting fertilization. The Cheung Lab
identified many vital proteins involved in this process. Mainly, these proteins include, FERONIA
(FER), LORELEI (LRE), and ANXUR (ANX). The surface receptor kinase FER was found to be an
upstream regulator of plant RHO GTPases (RAC/ROPs) and multiple transmembrane spanning
NADPH oxidases. The localization of FER to the membrane is highly dependent on the GPI–
anchored protein LORELEI–like–GPI–anchored protein 1 (LLG1). Proper interaction between FER
and LLG1 prevents ... Show more content on Helpwriting.net ...
Cheung uses many different approaches throughout her research. It is common to see the Cheung
Lab prove their findings extensively using multiple approaches to the same problem to ensure the
production of high quality work. Working with plants, the mapping of genes and generating mutants
plays a critical role in how plants are studied. By inserting genes of interest such as FER with a GFP
tag, fluorescence microscopy becomes a solution in observing the localization of FER during
different stages in the plants life as well as different conditions of its environment. In addition to
tagging proteins, the Cheung lab heavily relies on fluorescence microscopy to visualize many
different structures and molecules in different types of cells throughout the plant. With the
combination of fluorescence, confocal, and electron microscopy, the Cheung Lab can utilize
different approaches in overcoming the scientific challenges they face. Dr. Cheung clearly
demonstrated the interactions with FER to permit localization with LLG1 as well as membrane
embedding with LRE. The next step she would like to take in her research is to identify which
ligands interact with FER at the membrane and what effect do they have on FER localization, as
well the signaling effects downstream. Also, she will explore how these processes change in
different cell types throughout the

P1 / Hc Pro Of The Potyvirus Targets
P1/HC–Pro of the Potyvirus targets RISC assembly (Brigneti et al., 1998; Anandalakshmi et al.,
1998 ; Kasschau et al., 2003), 2b of Cucumber mosaic virus (CMV) binds to dsRNA and interferes
with spread of silencing signal (Brigneti et al.,1998 ; Qi et al., 2004), p19 of tombusviruses binds to
siRNAs (Voinnet et al., 1999; Silhavy et al., 2002 ; Qi et al., 2004), p38 encoded by the Turnip
crinkle virus binds AGO1 and inhibits the activity of DCL–4 (Thomas et al., 2003; Azevedo et al.,
2010), P25 of Potato Virus X interferes with the spread of silencing signal (Voinnet et al., 2000),
P23, S, γb, P15, P0, P1, P30, P69, NS and coat protein of closterovirus (Reed et al., 2003 ; Lu et al.,
2004), comovirus (Liu et al., 2004), hordeivirus ... Show more content on Helpwriting.net ...
Contrary to RNA viruses that can be controlled only by PTGS, geminiviruses may be manipulated
by both PTGS and TGS. TGS is introduced when siRNAs corresponding to the promoter regions are
produced that direct methylation of the promoter followed by inhibition of transcription (Mette et
al., 2000). In a transient assay, TGS was reported to be effective against the begomovirus Mungbean
yellow mosaic virus (Pooggin et al., 2003).
Viral invasiveness is reported to be promoted by the ability of C1 to suppress PTGS (Cui et al.,
2005). It has been shown that C4 gene of Cotton leaf curl Multan virus and βC1gene of Cotton leaf
curl Multan betasatellite bind short RNAs, with a preference for the double stranded and single
stranded forms, respectively, suggesting that these suppressors sequester siRNAs and prevent their
incorporation into the RNA–induced silencing complex (RISC) involved in sequence specific
mRNA degradation (Hammond et al., 2000).
V2, a unique protein of monopartite begomoviruses has been shown to suppress PTGS in transient
assays (Zrachya et al., 2007). It was demonstrated that ability of V2 to interact with SISG3, the
tomato homologue of Arabidopsis SGS3 leads to suppression of PTGS (Glick et al., 2008).
Furthermore, it was shown that the Rep proteins encoded by two alphasatellites, Gossypium
darwinii symptomless alphasatellite and Gossypium mustelinium symptomless alphasatellite possess
suppressor activity (Nawaz–ul–Rehman et

Essay On Arabidopsis Thaliana
The Whitehead Institute for Biomedical Research at MIT recently published a new study in which
the molecular activity of a critical protein is elucidated in depth. A research team at Whitehead used
metabolomics technology to accomplish this, analyzing a protein known to be responsible for
making plants resistant to herbicide. The team found that the protein is occasionally inaccurate, and
another team also found a means by which to re–engineer them to be more accurate at the
University of Zurich. The new study focuses on a protein that serves as either an enzyme or a
catalyst that was first sequestered in bacteria. It has since been added to soybeans and corn during
the 1990s. The new study takes that research to the next level, as ... Show more content on
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Plants' limitations frequently mean they have to contend with the environment using only the
internal biochemistry. "Although they appear to be stationary, plants have rapidly evolving
metabolic systems," Weng says. "Now, we can gain an unprecedented view of these changes because
of cutting–edge techniques like metabolomics, allowing us to analyze metabolites and other
biochemical on a broad scale." Weng's laboratory focuses on enzymes, which is significant because
enzymes play one of the most important roles in the process of evolution. Researchers in general
have looked at enzymes as naturally–occurring nanomachines in a manner of speaking because they
perfectly convert a substrate to whatever is most appropriate without fail–substrate being the surface
on which organisms live. Enzymes were believed to do the same to any starting material with the
same success rate, but Weng's findings illustrate that their success rate is far from being as
immaculate as initially thought. "This concept, known as enzyme promiscuity, has a variety of
implications, both in enzyme evolution and, more broadly, in human disease." Christ was still a
graduate student during the course of the study in Zurich, and his team found what it was looking
for in BAR, an enzyme engineered into plants long ago as a chemical biomarker to aid scientific
research.

Chloroplast Outline
Intro outline
Chloroplast function
Its movements: photorelocation
Importance of chloroplast location
Proteins involved with it
Correlation with light
How the light induces the protein In plants, chloroplasts function to conduct photosynthesis where
the photosynthetic pigment chlorophyll captures the energy from sunlight and converts it and stores
it in the energy–storage molecules ATP and NADPH while freeing oxygen from water. They then
use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the
Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis,
much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell
varies from one,

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

Amplified Using PCR Reaction From Rice Genomic DNA : Lab...
The Ramy3D promoter and 5′ UTR were amplified using PCR reaction from rice genomic DNA. As
shown in Figure 1, a 995 bp fragment was obtained from PCR reaction. The product sizes were
consistent with our expected length. The amplified fragment was ligated into the pTG19–T vector to
obtain pTG19–RamyPro recombinant vector. The pTG19–RamyPro vector was digested with BamH
I restriction enzyme to further confirm the cloning of the desired fragment. The digestion reaction
showed the correct insertion of the desired fragment into pTG19–T vector (Figure 2).
3.2 Promoter sequence analysis
The Plant CARE (Lescot, Déhais et al. 2002) database was used to identify cis–regulatory elements.
A total number of 50 cis elements belonging to 19 different ... Show more content on
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2007). Similarly, about 19% of promoters in rice contain the TATA–box (Civan and Švec 2009).
With regard to metabolically regulation of Ramy3D promoter by sugar in the embryo, the presence
of TATA–box in rice Ramy3D promoter core is consistent with the previous reports on yeast and
human in which the TATA–box is generally related to tissue specific expression and mostly
modulated by stress stimuli. Previously the transcription start site (TSS) of Ramy3D was mapped
(Lu, Lim et al. 1998). A dimer motif called YR Rule (C/T A/G) was identified at the transcription
start site (–1/+1) of both Arabidopsis and rice promoters (Yamamoto, Ichida et al. 2007). We also
identified the YR Rule motif with 'CA' sequence in TSS of Ramy3D (Figure 3). The CAAT Box is
another well conserved promoter core which has been found to play an important role in
determining the efficiency of promoter. Totally, 12 copies of CAAT–box were identified in the
promoter sequence.
There are some regulatory sequences such as enhancers, silencers, insulators, and cis–elements at
the proximal and distal regions of the promoter that are involved in the regulation of gene
expression at the transcriptional level (Hernandez–Garcia and Finer 2014). The expression of α–
amylase genes in both rice cell suspension and germinating embryos is inhibited by sugars and the
mechanism involves transcriptional regulation (Lu, Lim et al. 1998). Scanning the

Antagonism Between Ja And Cytokinin
Antagonism between JA and cytokinin is of common occurrence in various plant growth and
developmental processes. Cytokinin, benzyladenine (BA) has been reported to antagonize the effect
of JA on root growth promotion in Solanum tuberosum (Sarkar et al., 2006). In cotyledons of
sunflower (Helianthus annuus), MeJA promoted senescence, whereas pretreatment with cytokinin
partially blocked MeJA–induced senescence (Mukherjee et al., 2002). Liu et al. (2015) concluded
that exogenous applications of JA and cytokinin antagonistically regulated leaf senescence in O.
sativa senescence associated genes expression. They also proposed that leaf senescence not only
depends on the level of JA or cytokinin but also on the balance between JA and cytokinin (Liu et al.,
2015). Earlier, Ananieva and Ananiev (2003) argued that MeJA promoted some aspects of
senescence in intact Cucurbita pepo cotyledons partially due to down–regulation of endogenous
levels of cytokinine levels and interconversion between active and inactive forms of cytokines
(Ananieva and Ananiev, 2003). Apart from the above reports, antagonistic effect of cytokinins on the
stimulatory effect of JAs has also been observed in potato tuber formation under in vitro conditions
(Sarkar et al., 2006). A synergistic effect of JA and cytokinin has also been reported in T. aestivum
to alleviate effects of salinity stress.
5.4. Jasmonates and abscisic acid
Several physiological and developmental processes in plants are influenced by JA

The Crystal Structure Of H2A
. As one of the most conserved histone variants, H2A.Z constitutes around 15% of the total H2A
cellular pool (Jarillo & Piñeiro, 2015). H2A.Z diverged from H2A early in eukaryotic evolution, but
has remained extensively preserved across eukaryotes (Talbert & Henikoff, 2010). The crystal
structure of a H2A.Z–nucleosome core particle showed similarity to that of a nucleosome structure
containing canonical H2A (Figure 10). However, these distinct localized modifications result in
slight destabilization of the interaction between the (H2A.Z–H2B) dimer and the (H3–H4)2
tetramer. Moreover, H2A.Z–nucleosomes have a different surface that contains a metal ion (Mn+2).
This altered surface may cause modifications in higher order structure and could ... Show more
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In Drosophila, nucleosomes form context–specific barriers to transcription that can be tuned at least
in part by incorporation of H2A.Z (Weber et al., 2014). In murine embryonic stem cells, H2A.Z is
enriched at active enhancers and promoters and facilitates chromatin accessibility to allow binding
of a variety of active and repressive complexes required for self–renewal and differentiation (Hu et
al., 2013). Also, transcription–coupled H2A.Z changes may play a role in cancer initiation and
progression (Conerly et al., 2010). In human breast cancer cells, H2A.Z acts as an important player
for enhancer functions. H2A.Z organizes a chromatin environment required for RNA polymerase II
recruitment and enhancer–promoter(s) interactions, all essential features of enhancer activity
(Brunelle et al., 2015). In Arabidopsis, H2A.Z predominantly associates with genes at euchromatic
regions (Fig. 8A) (Coleman–Derr & Zilberman, 2012b; Sura et al., 2017; Zilberman et al., 2008). At
highly expressed protein coding genes, H2A.Z is intensely enriched around the nucleosome–
depleted region (NDR) at transcriptional start sites (TSSs), particularly at the +1 nucleosome (i.e.
the first nucleosome downstream of the TSS) (Coleman–Derr & Zilberman, 2012b; Sura et al.,
2017; Zhang et al., 2016; Zilberman et al., 2008) (Figure 8B). The +1 nucleosome can act as a
barrier to

What Is The Use Of QPCR Used To Determine The Amount Of DNA?
Being able to determine the amount of DNA present in an organism has been successfully done
using qPCR. In this experiment, qPCR was used to identify how much fungi could infect mutant and
wildtype lines of A. thaliana. Also, qPCR was used to amplify the 16s rRNA ITS (internal
transcribed spacer) of an unknown fungal pathogen. Other ways qPCR has been used in recent years
include the use of qPCR to quantify copy number variants in the HER–2 gene which is a proto–
oncogene. This method was particularly employed in the formalin–fixed–parafilm–embedded
tissues – due to the fact that their DNA is usually broken into smaller pieces – to gain accurate
results. This study concluded that qPCR produced similar results with already existing ... Show
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The mutated protein is seen to possess a leucine rich region (LRR) and a family of receptors known
as Toll/interleukin–1 receptor (TIR). We see from Kobe and Kajava (2001), that repeated amino
acids seem to be structurally and functionally important. Leucine rich regions are usually involved
in interactions with other proteins. LRRs are involved in several biological activities including
development in early mammals, interactions involving receptors and hormones, cell adhesion and
polarization, resistance to plant diseases and many others. Meyers et al. (2002), says that the TIR
domain possess three conserved regions and a stretch of 200 amino acids that may link TLR
receptors with signalling pathways. Plant resistant disease proteins (R–proteins) in Arabidopsis have
two large families and TIR domain belongs to one of them. LRR repeats located at the c–terminal
and a nucleotide binding site(NBS) are contained in many disease resistant genes (R–genes).
Additionally, some of these NBS–LRR resistance proteins contain TIR domains at their N–terminus.
These NLR proteins are immune receptors involved in intracellular downstream signalling which
plays a huge role in how pathogens are recognized and how quick the innate immune system would
respond to an infection (Narusaka et al., 2016). Therefore, when comparing the

DORN1
DORN (Does Not Respond to Nucleotides 1), DORN1, L–Type Lectin Receptor Kinase I.9,
LECRK–I.9 are synonymous. According to TAIR database, LECRK–I.9 is involved in protein–
protein interactions with RGD–containing proteins as potential ligands, role in cell wall–plasma
membrane adhesion and involved in Phytophthora resistance. The mutant dorn1 is defective in
LECRK I.9. DORN1, binds ATP with high affinity and is required for: ATP–induced calcium
response, mitogen–activated protein kinase activation, gene expression. Ectopic expression of
DORN1 increased the plant response to physical wounding. Choi et.al. (2014) demonstrated that
DORN1 is essential for perception of extracellular ATP and likely plays a variety of roles in plant
stress resistance ... Show more content on Helpwriting.net ...
A. tumefaciens (strain LBA4404) carrying pCAMBIA 1200 35S harboring oxDORN1 gen and A.
tumefaciens (strain LBA4404) carrying pCAMBIA 1200 35S empty vector were supplied by Dr.
Kiwamu Tanaka. Agro–infiltration on N. benthamiana leaves was made following the procedure of
De Felippes and Weigel (2009) and adapting the O.D. and time of the day for agroinfiltration. Four
weeks old N. benthamiana plants were agroinfiltrated. Three days after agroinfiltration, leaves for
inoculated with TSWV. A total of five greenhouse assays were performed in order to determine the
better setup to test effect of oxDORN1 on TSWV levels. The first three were to optimize the
experiment, the fourth and the fifth were to evaluate the effect. The final treatments consisted of a)
N. benthamiana inoculated with buffer phosphate; b) A. tumefaciens strain LB4404 pCAMBIA1200
empty inoculated with TSWV (O.D.600nm 0.40); c) A. tumefaciens strain LB4404 pCAMBIA1200
35s oxDORN1 inoculated with TSWV (O.D.600nm 0.45) d) N. benthamiana inoculated with
TSWV. Three plants per treatment, three leaves agroinfiltrated (# 5, # 6, #7) and three days after
were inoculated. The inoculated leaves were harvested at 3, 7 and 10 days post–inoculation (dpi)
and tested by ELISA. The results of the transient expression of oxDORN1 did not show any
differences in the level of N protein

Review Of Genome-Wide Analysis Of Trx Family In Cotton...
Discussion
This work provides the first report on genome–wide analysis and characterization of TRX family in
cotton genomes. We found that there are 150 genes in Gossypium hirsutum, 92 genes in Gossypium
arboreum and 81 genes in Gossypium Ramondii. According to domain number, GhTRX genes
divided into five subfamilies (TRX–A, TRX–B, TRX–O, TRX–ERp29 and TRX–TPR_1_2).This
result is in agreement with previous study in other species such as rice, Arabidopsis and
sorghum(Choi, Jeong, & Kende, 2004). In addition, the majority of TRX genes in upland cotton
belonging to subfamily TRX–A and TRX–B agreeing with previous studies in rice, maize, soybean
and poplar (ref) this finding suggested that these two subfamilies may be involved in diverse ...
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Depending on events, evolutionary origin of the GhTRX genes might undertake 2 evolutionary
stages; last 0.31 and 1.08 mya. Evolutionary in G. hirsutum happened after rice and Arabidopsis.
There were10 duplicated pairs in rice Thioredoxin gene family, its Evolutionary origin might
undertake 3 evolutionary stages; events were ranged from 9 to 70 MYA (Ref) whereas the genome
of the ancestor of Arabidopsis underwent a duplication event about 24–40 MYA, shortly after the
divergence from the cotton ancestor. Approximately 14% of paralogous pairs remain up to date
(Meyer et al., 2005). In general duplication of GhTRX happened after OsTRX and ATTRX and the
number of genes duplicated was lower than in rice and Arabidopsis; this May be due to loss of most
paralogues (Ref). GhTRX–A subfamily was largest amongst GhTRXs subfamilies; agreeing with
previous study in rice, Arabidopsis and sorghum (Chibani, Wingsle, Jacquot, Gelhaye, & Rouhier,
2009). High number of TRX–A members may be due to duplication (Nuruzzaman et al., 2012), this
explains multiple members of TRX–A family in G.hirsutum. GhTRX genes roles under different
stresses
Six GhTRX genes were selected randomly to analyze their function in specific tissue, leaf
development stages, phytohormones and abiotic stress. In specific tissue, all genes were highly
expressed in various tissues suggesting that these genes may have crucial functions in cotton growth
and development. These results agree with previous study in

Transporters Vary Between Eukaryote And Prokaryote...
transporters vary between eukaryote and prokaryote organisms, ABC protein shows highly
conservative amino acid domains within NBDs. However, NBD have three well studies motifs;
ATP–binding sequences for the phosphate–binding loop (P–loop or Walker A motif), walker B
boxes, and ABC signature, ex (LIVMYA), which is fix in between Walker boxes (Akifumi
Sugiyama, et al, 2006) Plant ABC transporters uses different nomenclatures to shape plant ABC
subfamilies, a consistent nomenclature with Human Genome Organization which are the more
acceptable and useable method. Plant ABC transporters comes into eight subfamilies; A, B, C, D, E,
F, G, and I. However, ABCH not included within this group, as not yet identified in plant system
(Verrier P J et al., 2008). Among eight groups of ABC transporter gene members, more genes
number found within ACBB, ABCC, and ABCD transporter group cross all plant species (Thomas
S. Lane et al., 2016). ABCB and ABCC reported to having role in export and import, cellular and
long distance, auxin transport (Geisler, M. and Murphy, A.S. 2006), D group involve in auxin efflux
(Strader and Bartel, 2011). AtRlI2 a member of E subfamily found to be interfering with RNA
pathway (Braz et al., 2004). A and F subfamily has not yet functionally characterized in plant system
(Verrier P J et al., 2008, for review). medi– ate the cellular and long–distance transport of the plant
hormone auxin. Auxin paly crucial role at different stages in plant architecture and

Role Of Exogenous Pgrs In Alleviation Of Fe : An Analysis
Role of exogenous PGRs in alleviation of Fe induced adverse effects Iron (Fe) is an essential
microelement for all living organisms including plants, and is responsible for several key
physiological functions. It plays vital roles in the electron– transport chains of photosynthesis and
respiration to accept and donate electrons (Conte and Walker, 2011). Due to a wide range of
anthropogenic activities, agricultural soils are continuously being contaminated with a myriad of
chemical pollutants. Since Fe is an essential micronutrient, it becomes contaminant only at the
higher concentrations in the soil. Owing to its significant toxic consequences in plants, Fe has been
one of the least studied metals and sustainable strategies for ... Show more content on
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The genotype difference in ethylene production was observed to be more pronounced in the second
and third leaves than in the first leaf. Bronzing intensity increased with increased ethylene
production. There was not any direct correlation between increased Fe concentration in the tissue
and bronzing intensity or with the ethylene production among the 16 genotypes tested. On exposure
of the intact plant roots to Fe2+ at a concentration of 300 mg L–1 in culture medium, little stress–
induced ethylene production was noticed. However, partial or complete de–rooting the plant led to
stress–induced ethylene production, signifying the exclusion of Fe2+ by the roots limiting its uptake
so that little Fe–induced ethylene is produced in the intact plant. Leaf tissue tolerance for Fe2+ may
contribute to genotype disparity in Fe toxicity tolerance of rice plants when roots are injured during
transplanting or exposed to toxic substances in the soil. Bacaicoa et al., (2011) have studied the
influence of exogenous application of auxin on the main root Fe–stress. The root application of
auxin to plants without shoot Fe functional deficiency activates the expression of genes encoding the
main Fe–physiological root responses

Phytoremediation: Using Plants To Combat a Stressed...
Phytoremediation: Using Plants To Combat a Stressed Environment
Plants have long been adapting the traits necessary to survive in a wide variety of stressful
environments – including areas of high salinity, extreme heat, drought, and freezing temperatures –
but now, using genetic modification, scientists have been able to expand the role that plants play in
the environment. With the advent of transgenic biotechnology, plants can be enhanced with qualities
that not only allow them to flourish in stressed environments but also allow them to be used in the
effort to alleviate certain environmental stresses. Phytoremediators, plants that are used to clean–up
soil in contaminated areas, can remove heavy metals, arsenic, petroleum, TNT, ... Show more
(Bentjen, 2002)
Phytoremediation is a naturally occurring process that was recognized and documented by humans
more than 300 years ago. (Lasat, 2000) Since this time, humans have exploited certain plants'
abilities to survive in contaminated areas and to assist in the removal of contaminants from soil.
However, true scientific study and development of these plants unique qualities was not conducted
until the early 1980's. (Lasat, 2000) At this time it was recognized that certain species of plants
could accumulate high levels of heavy metals from the soil while continuing to grow and proliferate
normally. (Lasat, 2000) Although research has been slow and tedious due to scientists' incomplete
understanding of the generalized cellular mechanisms of plants, the advent of new genetic
technology has allowed scientists to determine the genetic basis for high rates of accumulation of
toxic substances in plants. (Clemens et al., 2002) Using genetic engineering, scientists may soon be
able to exploit this characteristic to provide a faster more efficient means of removing contaminants
from the soil. Genetic

Arabidopsis: A Case Study
The immune system of Arabidopsis thaliana can be divided into two lines of defence. Initially,
pattern recognition receptors (PRRs) on the cell membrane detect pathogen–associated molecular
patterns (PAMPs), which leads to PAMP–triggered immunity (PTI) associated with basal resistance
that defends the plant cell from less adapted pathogens (Jones and Dangl 2006). Pathogens that are
able to surmount this initial immune response do so through the use of virulent effector molecules
that inhibit and suppress PTI, which, in turn, activates the second line of defence, effector–triggered
immunity (ETI) (Jones and Dangl 2006). ETI is achieved through the expression of numerous genes
involved in disease resistance (R genes) that subsequently encode nucleotide binding–leucine rich
repeat (NB–LRR) proteins that each recognizes specific effectors, which ultimately results in
increased basal resistance and possibly apoptosis in the case of a hypersensitive response (HR)
(Jones and Dangl 2006). The enhanced disease susceptibility1 (EDS1) gene is a crucial component
of ETI, as its gene product serves as a signaling intermediary between this initial ... Show more
Nuclear EDS1 is directly involved in signalling SA–dependent transcriptional reprogramming of
genes that code for defensive proteins in addition to regulating apoptosis (García et al. 2010). An
increase in cytoplasmic EDS1 due to export from the nucleus, on the other hand, suppresses this
immune response and promotes apoptosis in an acute ETI response wherein EDS1 is unbound from
PAD4 and instead forms a complex with itself (García et al. 2010; Wagner et al. 2013). As a result,
proper EDS1 levels in different compartments of the cell are necessary for mounting the most
efficient immune response to different pathogenic microbes with respect to resistance and
programmed cell

The Importance Of Gene Imprinting
Gene imprinting is an epigenetic phenomenon when two alleles of a certain gene are expressed at
different level depending on their parent–of–origin. Gene imprinting has been documented in
mammals and flowering plants. In the 1980s, biologists' attention to imprinting has greatly increased
due to the recognition of its importance during mammalian development [1]. Imprinted genes
regulate cell growth, cell signaling, cell cycle regulation, and influence nutrient acquisition and fetus
growth. In mammals, many imprinted genes are found in the placenta and brain, which is consistent
with growth and neurodevelopmental defects observed in human imprinting disorders [2,3].
In addition to mammals, gene imprinting is also found in flowering plants. ... Show more content on
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However, you are required to have at least one heading. Please ensure that either British or
American English is used consistently in your chapter.
The angiosperms (flowering plants) are the most diverse group of land plants, with over 250,000
species [5]. Double fertilization is a unique feature distinguishing angiosperms from their seed–plant
predecessors (gymnosperms). This feature might have provided angiosperms an evolutionary
advantage to become the dominant form of land plant life, although the selection force of this trait is
poorly understood.
Unlike animals that define all cell lineages during embryogenesis, plants are able to establish novel
cell fates throughout their entire life cycle, especially during sexual reproduction. Sexual
reproduction in flowering plants comprises of a process divided into three phases: sporogenesis,
gametogenesis and embryo–/ endosperm–genesis.
Sporogenesis is initiated in both male and female reproductive tissues. In ovule primordium, a
subepidermal nucellar cell differentiates into a megaspore mother cell (MMC), the MMC then
undergoes meiosis to form four haploid megaspores. Only one megaspore survives to become
functional megaspore (FM) and proceeds to gametogenesis, while the other three degenerate. In
stamen primordium, one subepidermal nucellar cell gives rise to a microspore or pollen mother cell
(PMC). The PMC then undergoes meiosis to form four haploid microspores which will continue to

Annotated Bibliography
Topic Proposal and Annotated Bibliography
Alexander Hynes
Creighton University
Topic Proposal
In my research paper, I will attempt to determine how the perception of light in phytochromes plays
a role in the development of plants. Specifically, I will look at how phytochromes play a role in the
growth and development of Arabidopsis thaliana. The paper will also look at how light perception
plays a role in phototropism and the immune systems of a plant. Finally, my paper will explore how
changing light conditions impact perception in phytochromes.
Annotated Bibliography
Arana, M. V., Sánchez–Lamas, M., Strasser, B., Ibarra, S. E., Cerdán, P. D., Botto, J. F., & Sánchez,
R. A. (2014). Functional diversity of phytochrome family in the control ... Show more content on
Helpwriting.net ...
Specifically, the authors looked at the effect that the red to far red light ratio had on branching in
Arabidopsis. The authors ultimately found that the effect that phytochromes had on branching varied
significantly depending on the environment that the plant was in. Through the observations of the
authors, this primary literature will be useful in helping me assess the effects that phytochromes
have in the development of branches in

The Roles of HMGA Proteins Essay
Despite a wealth of biochemical in vitro data on the HMGA proteins of various organisms, their
biological role in chromatin is still not convincingly clarified. Current evidence suggests that HMG
proteins serve a global role in chromatin by conferring a more "open" configuration to chromatin
regions that are more accessible to transcriptional regulators (Bianchi and Agresti, 2005; Catez et
al., 2004). In addition, there is massive evidence that HMGA proteins act as architectural factors that
facilitate assembly of functional transcription factor complexes (enhanceosomes) at DNA target sites
by various mechanisms. Several studies analysing altered expression levels of HMGA genes in
animals have demonstrated that the chromosomal HMGA ... Show more content on Helpwriting.net
...
Therefore, it is the overall aim of my PhD project to gain insight into the in planta functions of
HMGA proteins. The project will be performed in the laboratory of Prof. Dr. K.D. Grasser
(Regensburg University), whose research group is specialised on studying plant chromosomal
proteins. Towards the goal of elucidating HMGA function, a variety of experimental approaches will
be employed using as central tool Arabidopsis plants with altered levels of HMGA protein that will
be analysed in comparison to wild type control plants. The available data suggest that HMGA
proteins as cofactors assist the proper transcription of putative target genes (Grasser, 2003;
Klosterman and Hadwiger, 2002). To evaluate this assumption, (1) we intend to examine plants that
have reduced amounts of HMGA (T–DNA insertion mutants, amiRNA plants) as well as plants that
have elevated levels of HMGA (overexpression plants). Using these plants we will analyse (2) the
consequences of altered HMGA levels on plant phenotype and transcriptome. In addition, (3) the
spatial and temporal expression pattern of HMGA is examined as well as (4) protein interactions of
HMGA.
3. Work program and Methodology
WP1. Starting point of the project is the molecular analysis of Arabidopsis candidate DNA insertion
lines (obtained from the NASC stock center) harbouring T–DNA insertions in the gene encoding
HMGA. Typically seeds of a segregating population are

Letter To Rashad Hall
It is a pleasure to write a letter of recommendation on behalf of Rashad Hall. He is an excellent
student with great potential to succeed in dental school. Mr. Hall was in my freshman biology course
and what I remember of him from then is how polite and diligent he was. Since then I have seen him
grow into a competent student who is genuinely interested in all his courses and puts in the effort to
completely understand the concepts being studied. My colleagues in the department have all
remarked on how well he does in their classes. Mr. Hall approached me about working in my lab in
spring 2014 and did so without any compensation. He is disciplined and responsible, extremely
reliable and trustworthy and showed up every day to check on his plants.

Essay On Arabidopsis Thaliaa
Unlike animals, plants are sessile though having the ability to adapt adverse stresses in their
environment such as drought, cold, high salt, etc. When plants are stressed with these conditions,
ABSCISIC ACID (ABA) level is increased in plants. The ABA triggers the adaptive responses
which are required for the survival and productivity of plants. ABA is crucial phyto–hormone that
mediates 10% of total transcriptional factors (TFs), which is higher compared to other phyto–
hormones in Arabidopsis thaliana (Fujita et al., 2011). The vast numbers of genes which are induced
by environmental conditions are activated by ABA. Among those genes, the members of bZIP
family are expressed in ABA dependent manner during stressed conditions. ... Show more content
on Helpwriting.net ...
They are Conserved domain 1 (C1), C2, C3 C4, and bZIP domain. Conserved domains 1, 2, and 3
have phosphorylation sites, so that these proteins are phosphorylated by kinase. Members of Sucrose
Non–Fermenting 1 (SNF1)–Related protein Kinase 2s (SnRK2s) phosphorylate and positively
control the AREBs/ABFs TFs (Fujita et al., 2013). bZIP domain has two regions, basic region which
is responsible for DNA binding; and leucine zipper region responsible for homo or hetero
dimerization (Mark, 2002). MECHANISM OF AREBs/ABFs REGULATION Once the plants go
through abiotic stresses like drought, temperature, and salinity, ABA is produced to rescue the plants
from these harsh conditions. ABA evokes signal transduction pathway leading to the activation of
the members of SnRK2s, namely SnRK2.2, SnRK2.3 and SnRk2.6 (Fujita et al., 2013). The
SnRK2s leads the activation of downstream AREBs/ABFs. SnRK2s are responsible for ABA–
dependent phosphorylation of AREBs/ABFs in multiple phosphorylation sites (RXXS/T) in protein
sequence (Figure 2) (Nicolas et al., 2014). AREB1/ABF2, AREB2/ABF4, ABF3, and ABF1 are the
major TFs which are downstream of ABA–activated SnRK2s in ABA signalling pathway during
vegetative growth. ABA and abiotic stresses induce gene expression through cis elements which
include ABA response element (ABRE) in their promoters. AREBs/ABFs bind to the ABRE
containing promoters in vitro or in yeast (Choi, et al., 2000; Finkelstein et al., 2000). ABRE is

The Importance Of Epigenetic Mechanisms In Eukaryotes
In eukaryotes, in addition to proven roles of regulatory components, epigenetic mechanisms have
emerged as significant factors in conferring environmental adaptability. In spite of the clear role of
chromatin structure in controlling gene expression in eukaryotes (Haig, 2004), the relevant
mechanisms involved in regulating Pi transcriptional networks has not been fully investigated. In
response to environmental signals, epigenetic mechanisms can affect the chromatin landscape by
altering its biochemical properties and promote rapid reactivation of numerous stress response
genes. An understanding of chromatin structure and the epigenetic mechanisms that modulate DNA
and chromatin may help to elucidate the impacts of chromatin level changes ... Show more content
For example, mutation in two Arabidopsis genes that encode flowering time regulators, FCA and
FPA, exhibited defects in flower development due to RNA–mediated chromatin silencing of a range
of loci in the genome including the Phytoene Desaturase (PDS) gene. This suppression was
accompanied by the asymmetric methylation of the endogenous PDS locus. These data suggest that
FCA and FPA regulate chromatin silencing through interaction in a locus–dependent manner with
the siRNA–directed DNA methylation pathway to regulate common targets (Bäurle et al., 2007).
Figure 4. Overview of possible epigenetic modifications. These epigenetic modifications can all
influence the accessibility of the chromatin structure to the transcriptional machinery. This image
was taken from a previous publication (Gräff et al., 2011).
DNA methylation
Cytosine DNA methylation is a major epigenetic mark in both plants and animals that tends to
generate heterochromatin structure, which leads to gene repression. DNA methylation is not evenly
distributed across the genome but rather is enriched at repetitive DNA elements like transposons,
whereas most genes have limited methylation or are unmethylated (Zilberman et al., 2007). In
plants, three distinct types of methylation occur based on sequence context. These include CG, CHG
and CHH site classes, which are established and maintained by separate enzymatic pathways
(Bewick et al., 2016). Several studies have

Essay On Rice
Salt stress results to stunted growth and reduced productivity of rice. Transcription factors like heat
shock factors (HSFs) represents key controllers of stress adaptation. Moreover, heat shock factors of
the group A and B are clearly established as thermal and non–thermal stress controllers in many
plants. Therefore, this experiment aims at examining the functions of OsHsfC1b transcription factor
in rice. There are several transcription factors that work in rice, including MYB, NAC and bZIP,
leading to regulation of the stress– responsive genes in the crop. In addition, Bahadur et al. (2015)
reveal that the Heat Shock factors (HSFs) are kind of transcription factors that are categorized into
three groups: A, B and C. these groups of ... Show more content on Helpwriting.net ...
OsHsFa2e and OsHsf7, have been confirmed to functionally work in vivo. Transgenic crops, such as
rice, with expressing OsHsfA2e are known to be more tolerant to the heat and stress than any other
plants.
BLAST search and multiple cycle alignment of OsHsfC1b (Os01g53220) show that homologous
proteins are found in other monocots such as sorghum, maize and Brachypodium, but also in the
dicot Arabidopsis. In rice, OsHsfC1b shares highest similarity with OsHsfC1a, another member of
the four class C HSFs identified in rice (Arvidsson et al, 2008, p. 211). Proteins hold a well
preserved N–terminal DNA– binding domains that has four β–sheets and α–helices and a highly
conserved oligomerization domain also known as HR–A/B domain. Putative nuclear localization
signal upstream of the oligomerization domain was found in all proteins (Gupta, Palma, & Corpas,
2016). A subcellular localization study was conducted to confirm targeting of OsHsfC1b to the
nucleus in Arabidopsis mesophyll cell protoplast.
Hypothesis
In this study, rice will be exposed to osmotic stress condition, whereby it will show: a higher
accumulation of proline and soluble sugars, reduced levels of MDA and minimized water loss rate
compared to wild types of plant. Still, the stress–responsive gene OsHsfC1b will exhibit a
significantly higher expression levels in rice than in transgenic plants under similar environmental
conditions. Although OsHsfC1b has been evaluated purposely for its significance in drought

Determination Of Flowering In Arabaliana
Affects of Vernalization Length on the Flowering of Arabidopsis thaliana
Background information
The flowering of plants is a tightly controlled process and flowering at the wrong time could cause
detrimental problems for a plant, especially if it were to flower too early in the season. There are
both environment and genetic factors that can influence flowering in Arabidopsis thaliana. In the
winter–annual A. thaliana, environmental factors affect the gene expression of Flowering Locus C
(FLC) (Michaels, et al., 2006). Environmental factors include the quality and quantity of light and
vernalization, which is the promotion of flowering due to cold temperatures (Balasubramanian et al.,
2006). Genetic factors include FRIGIDA (FRI), flowering ... Show more content on Helpwriting.net
...
Two will be the control with a normal period of vernalization at five weeks, two will be in a short
vernalization period at three weeks, two will be at a relatively long period of vernalization at seven
weeks, and two will be at the longest period of vernalization of nine weeks. The independent
variable will be vernalization length, and the dependent variable will be the time it takes the plants
to flower. The vernalization will occur at 4ºC. Otherwise; they will be grown at 23ºC. Before
vernalization, they will grow at normal temperature for four weeks. Other constants include light, at
20–150 µmol/m2sec and humidity, at 55%. The plants will be grown in long day periods of fourteen
hours of light, with dawn at 0600 hours and dusk at 2000 hours. For accurate results, the plants will
be grown in a growth chamber. After their first vernalization, I will grow them at 23ºC for four
weeks, then put them in a vernalization state again, but each for one less week than previously done.
I will repeat this same process twice so that I can shorten the vernalization time again. Flowering
time will be measured in days since initial planting to the first

Arabidopsis Climate Change
Climate change is a crucial issue which every living organism in this planet should cope with. Plants
are in a disadvantaged position because they cannot move, like other organisms for avoiding the
effects of the global warming. Thus, they should find ways to adapt to these changes, even when
they are in very harsh environments, like in high altitude habitats. The effects of climate change
could alter the functional traits and the phenology of the plants. This review article deals with the
differences of the flowering time of Arabidopsis thaliana in low and high altitudes and also with the
alteration of this due to the effects of global warming. As it is already discussed in the previous
paragraphs, the flowering time of Arabidopsis thaliana

Why Phenotypic Plasticity Is Present
Introduction
The plants used in this experiment were the Arabidopsis thaliana. The Arabidopsis species is
characterized as a "weed", a plant with no benefit when it comes to food, shelter, or medicine
(Meinke & Koornneef, 2010). Yet, it is considered the model research plant by many scientists
across the world because they are small and can grow very fast. Meinke and Koornneef (2010)
explain that scientists want to be able to collect as much data as quickly as possible, so a small, fast
growing plant is going to help make discoveries much more rapidly than a longer growing crop
plant. The Arabidopsis plant is also very convenient to study its genes because of its small genome.
A small genome makes it efficient to see how a plant's genes ... Show more content on
Helpwriting.net ...
Lutz et al. (2015) state that plants integrate seasonal cues such as temperature and day length to
optimally adjust their flowering time to the environment. The knowledge about the adaptation of
plants to changing temperatures at present is limited, but becoming increasingly important due to the
temperature changes associated with global warming (Lutz et al. 2015). This leads to a hypothesis
that as temperature increases, rosette size and height of plant will decrease.
Methods
24 plants of the species Arabidopsis thaliana were grown at two temperatures (20°C and 24°C) in
Percival growth chambers, half at 20°C and half 24°C. The plants were randomized into a design
that consisted of 12 flats in two growth chambers. The seedlings were then transferred to three inch
pots on standard ProMix potting soil and bottom watered in their trays, two times per week to assure
that the potting mix remained moist. Each group will have two different accessions; Natural
Population A and Natural Population B. Natural Population A represents species extracted from
Market Baden, Germany. Natural Population B represents species extracted from Merzhausen,
Germany. Each accession will have six plants growing under 20°C and 24°C. All 24 plants were
then looked at to measure the rosette size, the distance from the center stalk to the edge of the
leaves. All measurements were reported in centimeters using a ruler. The plants were measured in
two spans that were

Arabidopsis Thaliana
Science is a study that prides itself in being in being an intellectual subject, it would only be right
that its representatives (professors in this case) be efficient when describing subjects that have a
large area to cover. This requires using easier concepts to understand and that can be applied to a
greater area. One way of doing this is through organisation. If you were a taxonomist, would you
start at describing animals by every different Genus and Species? No! You would start at their
Kingdom and Phylum, then work your way down. Every one of these different species is an
excellent representation of a broader group of life. These seven are vast in the number of different
species they represent.
Escherichia coli, also known as E.coli is ... Show more content on Helpwriting.net ...
80 years ago this animal was able to provide a definite proof that genes are carried on chromosomes.
By editing the DNA of this animal, scientists noticed that certain areas of the fly grew differently (a
leg on its head) causing mutant flies. With this information, they were able to understand better the
cause and effect from the genetic instructions encoded within the chromosomal DNA to the structure
of the adult multicellular

A Transgenic Lines
Three independent homozygous transgenic lines with significantly higher Os08g01480 expression
were selected for further characterization. In early stages of vegetative growth on
Soilrite, no phenotypic difference was observed in transgenic lines in comparison to WT.
However, there was clear difference in bolting time between WT and transgenic lines
(Supplementary Fig. S2). The visible changes in early plant growth between WT and transgenic
lines were analyzed through measuring root length after growth on ½ MS plates for 11 days. All the
transgenic lines showed significantly increased root length compared to
WT plants. To study whether increase in root length was due to early germination, germination rate
of WT and transgenic lines was ... Show more content on Helpwriting.net ...
At the same time, significantly lower (~25%, 20%, 40%, and
7%, decrease) root length inhibition in transgenic plants was recorded in comparison to root length
of NT transgenic plants. (Fig. 1).
For salt and osmotic stress, WT and transgenic line were grown on NaCl (50 mM) and mannitol
(150 mM) for 11 d. Root length of WT showed significant decrease (70%) as compared to
transgenic line (30%–50%) during salt stress as compared to NT; WT and transgenic seedlings,
whereas in osmotic stress, ~50% and up to 40% decrease was observed in WT and transgenic lines
compared to NT; WT and transgenic plants. It is concluded that in WT there was ~40% and 20%
more reduction in case of salt stress and osmotic stress respectively (Fig. 2).
For studying effect of cold and heat, after stratification seeds were kept at –20˚C and
37˚C respectively for 4 h and then transferred to control conditions. As much as ~60% and
40% decrease in root length of WT was noted during cold and heat stress, respectively when
compared to NT; WT plants, while ~25% and ~15% decrease of root length was recorded in
transgenic lines at time of heat and cold stress, respectively when compared to NT transgenic plants.
This result indicated ~40% and ~20% reduction in root length of WT compared to transgenic lines
subjected to cold and heat stresses (Fig. 3). These studies

Eukaryotes: Epigenetic Analysis
Veluchamy et al., (2016), found DNA and histone associations in Eukaryotes plays role in chromatin
compaction and in shaping three dimensional topology of the genome. He and his colleagues did an
experiment on the role of LHP1 in H3K27me3. PcG which is mentioned as one of the earliest
epigenetic regulatory mechanism remodel chromatin such that epigenetic silencing of genes happen.
The PcG identified the repression of HOX genes in Drosophila melanogaster. The HOX genes are
group of related genes which are in contention of controlling body plan like the embryo. Earlier
there are claims on the complex nature of PRc1 and PRC2. Arabidopsis has three PRC2 genes based
on the presence of the three animal suppressors of zeste 12 (SU (Z) 12) homologous ... Show more
1B, they used a hexagonal binding routine to show where LHP1 and RNA pol II joined which gave
the authors a good dimension of differentiation of overlapping points based on count. As shown on
the figure the Y axis belongs to the H3K27me3 and the X–axis belongs to RNA pol II which helped
them to compare the midpoints of the gene. Based on the result they identified 8,882 genes by LHP1
but most of them are not related to RNA pol II. However, in fig C, hexagonal binning of LHP1 and
H3K27me3 revealed there is a strong association between the two. Points in fig. 1C, shows the
distance from the midpoints of the gene to the nearest gene. Fig. 1D. shows the average CHIP–seq
enrichment profiles of H3K27me3 and LHP1 in WT which is stratified by the gene length. They
also did spin algorithm over genes and flanking 2kb region for

Arabidopsis Thaliana Report
Title
Occurrence of microRNA expressions using various nutrient deficiencies presented to Arabidopsis
thaliana
Introduction
Arabidopsis thaliana is the model organism chosen for investigation of miRNA expression because
its entire genome has been sequenced (Weems 362–369). This organism also has a short life cycle
and grows relatively quick with restricted space and this also makes it useful for lab research
(Weems 362–369). The nutrient concentrations that were observed in this study included phosphorus
and sulfur. These nutrients are specifically used because they are considered macronutrients that are
required for plant growth (Axtell). Phosphorus is a component of nucleic acids, phospholipids, ATP
and coenzyme. Sulfur is also a component ... Show more content on Helpwriting.net ...
The control in this experiment was the full media plate. The independent variable manipulated in
this study was the media type that the seeds were grown on. The dependent variable measured was
the varying levels of miRNA expression. I did a full media plate. The plates were then allowed to
grow for two weeks. The full media plate was used in comparison to the low phosphorus and low
sulfur plates. After growth the plants were collected with sterilized tweezers and grinded using a
lysis mix and a pestle. Next, the kit used for isolating the small RNAs was a Sigma mirPremier
microRNA isolation kit following the manufacturer's protocol. The microRNAs were then run in the
thermocycler performing reverse transcription reactions to convert the RNAs into single–stranded
complementary DNAs. Reverse Transcriptase Master Mix was used for the reverse transcription
reactions. Lastly, quantitative real–time polymerase chain reaction (qt–PCR) was used to analyze the
microRNA levels. Four microRNAs were examined for each media type. Every media type was
analyzed using this procedure and U6 was used as the reference gene for analysis. A U6 Master mix
and miRNA master mix were used for analysis of each media type. The four primers used for
analysis were miR156, miR395, miR398 and miR399. The efficiency values, E, were then obtained
from the previous study (data

The Network Of Polymeric Structure
The cytoskeleton, network of polymeric structure is a highly dynamic framework comprised of
microtubules polymerized from α– and β–tubulin subunits and microfilaments (AFs) polymerized
from G–actin and related proteins. Numerous studies have shown the presence of cross–bridges
between cortical microtubules and the PM, so they maintain a link and this linkage can extend to the
cell wall (Akashi et al., 1990; Akashi and Shibaoka, 1991; Shibaoka, 1994; Sonobe and Takahashi,
1994). Plant cytoskeleton maintains proximity with the plasma membrane that provides an
important platform for signal perception and transduction (Gilroy and Trewavas, 2001; Wasteneys
and Galway, 2003). Above described proximity concept suggests this framework as a downstream
targets of various signalling pathways. The bond arises between plasma membrane and cytoskeleton
through a hydrophobic domain which present on the tubulin molecule or indirectly through
interaction with an integral membrane protein (Sonesson et al., 1997). Phospholipase D (PLD) is a
plasma membrane protein which has been characterized and confirmed for having the ability to
make connection between cortical microtubules and the plasma membrane (Gardiner et al., 2001;
Dhonukshe et al., 2003; Drobak et al., 2004; Hong et al., 2008). Therefore PLD has been suggested
to function as a structural and signalling link between the plasma membrane and the cytoskeleton in
Arabidopsis in tobacco (Gardiner et al., 2003). Cytoskeletal reorganization

Essay On Pia
Many reports have clearly demonstrated the roles of phytohormones in Pi signaling pathways
(López–Bucio et al., 2005; Nacry et al., 2005). Previous work has shown that Pi starvation in plants
caused a reduction in Gibberellic Acid (GA) levels and accumulation of DELLA proteins. DELLA–
mediated signaling contributes to certain aspects of Pi–deficiency responses in roots, i.e.
suppression of primary root growth and raise of root hairs (C. Jiang, Gao, Liao, Harberd, & Fu,
2007). Auxin is known to control GA–mediated repression of two growth–repressor DELLA
proteins known as RGA and GAI (Fu & Harberd, 2003). Furthermore, it was shown that ethylene
and strigolactone biosynthesis is induced in response to Pi deficiency (Nagarajan & Smith, 2011). ...
Show more content on Helpwriting.net ...
In higher plants, four Pi transporter (Pht) families have been characterized (Pht1–Pht4) (B. Guo et
al., 2008; Lin, Lin, & Chiou, 2009; Nussaume et al., 2011; Poirier & Bucher, 2002; Versaw &
Harrison, 2002). Many members of the Pht1 family play important roles in Pi acquisition from soil
and root–to–shoot translocation of Pi (Nussaume et al., 2011). The single Pht2 family member,
Pht2;1, is a low–affinity Pi transporter localized to the chloroplast envelope where it plays an
important role in photosynthetic activity (Rausch, Zimmermann, Amrhein, & Bucher, 2004; Versaw
& Harrison, 2002). The Pht3 family is comprised of mitochondrial–localized transporters to provide
Pi for the oxidative phosphorylation of ADP to ATP (Nakamori et al., 2002; Poirier & Bucher,
2002). Pht4 transporters are low–affinity transporters that localize to plastids and Golgi (B. Guo et
al., 2008). The cooperation among the four Pht families allows plants to maintain Pi homeostasis
(Figure 3). Regulatory components involved in Pi signaling and Pi homeostasis in plants Plants have
evolved to react to fluctuations of Pi levels by means of complex responses that tightly control
intercellular Pi levels. These responses are initiated and modulated by elaborate signaling networks
that maintain Pi homeostasis via global

142S Primers
RESULTS
3.1 C24 and 142S have similar DNA sequences
The results from this experiment are inconclusive as the 1% agarose gel using 142S primers did not
display any bands (data not shown). The 142S transgene should be present in the 142S line only. In
the control gel (Fig 3), there are bands in every lane; actin is used as the loading control, showing
the PCR and gels were run according to standard procedures.
Figure 3. 1% agarose gel using actin primers shows constitutive bands in both C24 and 142S lines.
Lanes are independent samples, loaded as follows: 1 – 2log ladder; 2, 3, 4, 5, 6 – C24 (WT); 7, 8, 9,
10, 11 – 142S; 12 – Negative control (no plant DNA). Actin primers act as a positive control by
binding to a part of the genome present ... Show more content on Helpwriting.net ...
There is no significant difference in growth rate between C24 and 142S, t(12.9)=–0.098, p=0.923.
There is a significant difference in growth rate between Col–0 and SOS, F(3,36)=16.4, MSE=0.049,
p=0.000; Dunnett's test reveal that Col–0 is significantly different to SOS2 (p=0.000) and SOS3
(p=0.000) and similar to SOS1 (p=0.988). This follows a similar pattern in 142S and SOS; there is
significant difference in growth rate, F(3,35)=9.46, MSE=0.071, p=0.000; Dunnett's test reveal that
142S is significantly different to SOS2 (p=0.006) and SOS3 (p=0.019) and similar to SOS1

Arabidopsis Thalian The Role Of Evolution In Species
Evolution is reoccuring, the world changes little by little, day by day. Evolution is the mere evidence
of changes in the environment and the organisms inhabiting it. It is the biology in earth's history.
The measurement of evolution varies on each organism. Some organisms evolve at a faster rate and
some gradually change depending on their fitness rate to be able to survive varying environments
and timelines.
One example of evolution in species today is the mustard plant " Arabidopsis Thaliana". According
to Charles Darwin, "mutations are a raw material of evolution," meaning that those organisms better
fit for the ever–changing environment will most likely have the strongest type of DNA to be able to
pass on to its offspring and allow its species to successfully survive. And he recognizes these
differentiations occur due to new mutations in an organism's genome(1). The entire genome of the
"Arabidopsis Thaliana" was compared already in just a few years twenty DNA building blocks were
mutated in each of the five family lines. The rate of transformation there is faster than usual for it to
mutate that amount of DNA building blocks in such a short amount of time. ... Show more content
It is the gene for a protein that all humans have. It is called "Apolipoprotein AI" Its function in the
body system is to transport cholesterol through the bloodstream. This reduces heart disease because
it allows it removes arterial clogging. The small community in Milano, Italy known to carry the
mutant version of this protein have eighty–eight percent lower risk of any heart disease. Less people
in the hospital for heart attacks, strokes, etc(2). This is an example of evolution because while many
in the US are dying off with heart disease being on of the main cause of death in the country, the
people in Italy are benefiting from the advantage of this certain protein elongated their lifespan for
their

The Importance Of Green Fluorescent Protein
In the 1960's, Green Fluorescent Protein was discovered to be responsible for Aequorea victoria's
fluorescence under UV light (Niwa et al., 1996). Today, GFP is often used in protein tagging and has
made it possible for scientists to study expression and track proteins in vivo. With the rising
importance of GFP fusion proteins and other recombinant vectors, the metal affinity of Histidine
helps to make the protein purification process easier (Lilius et al., 1991). His tags are commonly
used to purify proteins through immobilized metal–affinity chromatography (IMAC) (Lilius et al.,
1991). This rapid and efficient method separates the recombinant protein from unwanted products
such as RNA. The His tag DNA sequence is inserted into the ... Show more content on
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It is of strong interest to molecular biologists because of the strong light emission of 508 nm under
UV light. UV wavelengths excite the fluorophore, contained in the Ser – Tyr – Gly sequence near
GFP's N–terminus, and a bright green fluorescence is given off as a result (Niwa et al., 1996). GFP
can be successfully tagged to many proteins without disturbing their function (Feilmeier et al.,
2000). This allows scientists to exploit the protein for its usefulness in marking proteins in vivo.
GFP tagging has many applications. It can be used to study gene expression by inserting gfp after a
promotor in the plasmid, so that if expressed, the colony expressing the gene of interest can be
identified by a green fluorescence of GFP under UV light (Feilmeier et al., 2000). Specific cellular
organelles can be tagged, such as the endoplasmic reticulum, to visualize protein localization and
networking inside the living cell. GFP can also be used to monitor cofactor levels within a cell in
real time. For example, when GFP was tagged to proteins that contain a receptor sensitive to Ca2+,
they interacted in a way so that the fluorescence of the fusion protein was proportional to the
calcium ion concentration with less than a 1 second lag in the cell (Romoser et al., 1997).
Throughout the decades, GFP mutants have been created to give brighter emission and different
wavelengths. Researchers can track separate cell pathways at the same time, since different proteins
can

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

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