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molecular genetics
"Being an educated person requires- being a full
person, requires a certain ability to deal with dissonance.
You know,
I’m Jewish, was raised Jewish.
I brought up my kids in the Jewish
tradition.
We celebrate Jewish traditions.
At the same time,
I’m a scientist.
And data means an awful lot to me.
And I
clearly believe in evolution and it’s really hard to get away from the
undirected nature of change selected by environment and, you know, the science
I do has really, leaves very little room for purpose in evolution."
Eric Lander
Molecular genetics is primarily concerned with the
inter-relationship
between information macromolecules DNA
(deoxyribonucleic
acid) and RNA (ribonucleic acid) and
how molecules are used to
synthesize polypeptides.
As the vast majority of gene expression is
dedicated to polypeptide
synthesis, proteins are the major functional end-points of the DNA template
and account for the majority of the dry weight of a cell.
The term
protein is derived from the
Greek proteios, meaning 'of the first rank' and reflects the important roles of
proteins in diverse cellular functions as enzymes, receptors, storage proteins,
transport proteins (tRNA), transcription
factors, signaling molecules, hormones, etc.
Proteins are
composed of one or more polypeptide
molecules which may be modified by the addition of various carbohydrate
side chains or other chemical groups.
Like DNA and
RNA, polypeptide molecules are
polymers consisting of a linear sequence of repeating units, in this case
amino acids.
The
latter consist of a positively charged amino group and a negatively charged
carboxylic acid (carboxyl) group connected by a central carbon
atom to which is attached an identifying
side chain.
Charged molecules are highly
soluble in water.
Both
DNA and RNA are
negatively charged (polyanions) because of the
organophosphate
charges present in their component nucleotides.
Depending on their
amino acid composition, proteins
may carry a net positive charge
(basic proteins) or a net negative charge (acidic proteins).
The
hydrogen bonding potential
of water molecules means that molecules with polar groups (including DNA,
RNA and proteins) can form multiple interactions with the
water molecules, leading to their
solubilization.
Thus, even electrically neutral proteins are often
readily soluble if they contain an appreciable number of charged or neutral
polar amino acids.
The
linear backbone of a DNA
molecule and of an RNA molecule consists of
alternating sugar residues and organophosphate groups.
Whereas
the RNA molecules within a cell normally exist as single molecules, the
structure of DNA is a double helix in which two
DNA molecules (DNA
strands) are held together by
weak hydrogen bonds
to form a DNA duplex.
DNA can adopt different types of helical
structure.
Genetic information is encoded by the linear sequence of
bases in the DNA strands (the primary structure).
Intermolecular
hydrogen bonding permits RNA-DNA duplexes and double-stranded RNA formation
which are important requirements for gene expression.
Hydrogen bonding can occur between bases
within a single DNA or RNA molecule.
The biological
features of this new system demonstrate it
can be engineered to edit the
genomes of human cells.
During the process of
DNA synthesis (DNA
replication), the two DNA strands of each chromosome are unwound by a
helicase enzyme and each DNA strand directs the synthesis of a complementary
DNA strand to generate two daughter DNA duplexes, each of which is identical to
the parent molecule.
DNA
replication is initiated at specific points, which have been termed origins
of replication.
According to their needs, different cells transcribe
different segments of the DNA (transcription units) which are discrete units,
spaced irregularly along the DNA sequence.
Only a portion of the RNA
made by transcription is translated into a polypeptide.
Infection of
receptor-bearing cells by coronaviruses is mediated by their spike (S)
proteins.
The coronavirus (SARS-CoV) that causes severe acute
respiratory syndrome (SARS) infects cells expressing the receptor
angiotensin-converting enzyme 2 (ACE2).
Here we show that codon
optimization of the SARS-CoV Spike protein gene substantially enhanced
S-protein expression.
We also found that two
retroviruses, simian immunodeficiency virus (SIV)
and murine leukaemia virus, both expressing green
fluorescent protein and pseudotyped with SARS-CoV Spike protein or S-protein
variants, efficiently infected HEK293T cells stably expressing ACE2.
Infection mediated by an S-protein variant whose
cytoplasmic domain had been truncated and altered to include a fragment of the
cytoplasmic tail of the human immunodeficiency
virus type 1 envelope glycoprotein was substantially more efficient than
that mediated by wild-type S protein.
SARS-CoV is not closely related to
any of the three previously defined genetic and serological coronavirus groups,
although it may be distantly related to group 2 coronaviruses.
SARS-CoV
spike (S) protein, a surface
glycoprotein that mediates coronavirus entry into receptor-bearing cells,
is also distinct from those of other coronaviruses.
The gene encoding
the S protein of SARS-CoV contains many codons used infrequently in mammalian
genes for efficiently expressed proteins.
We generated a
codon-optimized form of the S-protein gene and compared its expression with the
S-protein gene of the native viral sequence.
S protein was readily
detected in HEK293T cells transfected with a plasmid encoding the
codon-optimized S protein.
No S protein was detected in cells
transfected with a plasmid encoding the native S-protein gene.
When transfected cells were infected with
recombinant vaccinia virus expressing T7
polymerase, which can transcribe message in the cytoplasm, S protein was
efficiently produced from plasmids containing either codon-optimized or native
genes.
The codon-optimized gene expressed more than twice as much S
protein as the native viral sequence.
S protein could be efficiently
expressed from the codon-optimized plasmid without T7 polymerase, we used this
plasmid in our subsequent studies.
The
expression of genetic information in all cells is mostly a one-way system: DNA
specifies the synthesis of RNA and RNA specifies the synthesis of polypeptides,
which subsequently form proteins.
Because of its universality, the DNA
> RNA > polypeptide (protein) flow of genetic information has been
described as the central dogma of gene expression molecular biology.
The
shape and structure of proteins is a crucial aspect of molecular gene
expression and links our understanding of gene expression to the biology of the
cell.
While primarily concerned with protein molecules that act on DNA
and RNA sequences, such as transcription factors and histones, the study of
gene expression also focuses on where in the cell expression is
modulated.
In fact, the modulation of gene expression can occur in the
nucleus, the cytoplasm, or even at the cell membrane due to the impact of
proteins on RNA in those cellular subregions.
In his Nobel lecture,
given shortly after he joined the Rockefeller Institute
for Medical Research, Edward L. Tatum outlined the concepts fundamental
to his one-gene, one-enzyme (understood today as one-gene, one-polypeptide)
hypothesis:
all biochemical
processes in all organisms are under genetic control;
biochemical
processes are resolvable into a series of individual reactions;
each
reaction is controlled in a primary fashion by a single gene - 1:1
correspondence of gene and biochemical reaction exists;
mutation of a
single gene results only in an alteration in the ability of the cell to carry
out a single primary chemical reaction.
Geneticist George W. Beadle and
the biochemist Edward L. Tatum were awarded the Nobel Prize largely through the
auspices of the Rockefeller Foundation, for
this hypothesis which turned out to be
entirely false !!!
A cell uses the DNA molecule in the nucleus as
a template for protein
production.
The cell sends a 'messenger RNA' =
mRNA into the nucleus to retrieve the encoding.
The mRNA takes the
copied "recipe" out of the nucleus to the ribosome, which is where proteins are
made.
In eukaryotic cells (the kinds of cells found in plants and
animals), however, something very interesting happens before the mRNA leaves
the nucleus.
Some parts of the mRNA are cut away, and the remaining
parts are then stitched back together.
The parts of the mRNA that are
cut away never leave the nucleus, so they are called introns (they stay IN the
nucleus).
Introns regulate the amount of the various proteins that are
being made.
"For a while, geneticists didn't know the purpose of
introns, so in typical evolutionary fashion, many decided that they had no
purpose, and introns were lumped into the category of "junk DNA." As we have
learned more about genetics, we have learned that the evolution-inspired idea
of "junk DNA" is, itself, junk, although some evolutionists still cling to it."
- Jay L. Wile
The remaining parts that are stitched together are called
exons (they EXit the nucleus).
Each exon represents a "module" of useful
information.
If the cell stitches the exons together in one way, it
makes one protein.
If it stitches the exons together in another way, it
makes a different protein.
As a result, a single gene can actually produce
many different proteins.
ALL of
molecular biology is based on this
fatal error.
Genetically modified organisms and the industrial
manipulation of molecular genetics is based on a theory that has turned out to
be entirely false.
Unintended toxic proteins is the
transgenic standard !
mRNA vaccine delivery using lipid
nanoparticles
The promise of activating the humoral and the
cellular arms of the immune
system has driven the development of DNA vaccines over the last decades.
Live-attenuated vaccines are the most potent in activating both
cellular and humoral immunity.
However, these vaccines exhibit
considerable safety drawbacks.
Attenuated
pathogens have the potential to revert to a pathogenic form.
DNA
therapeutics have to reach the nucleus, while for mRNA therapeutics, the
cytosol is the target.
DNA and mRNA vaccines share many
similarities.
The main difference between the two approaches is the
target location for the delivery of the oligonucleotides.
mRNA vaccines
have generated significant interest to replace traditional vaccines due to a
number of important attributes that they possess.
mRNA vaccines elicit a
potent immune response including antibodies and cytotoxic T
cells.
Successful cytosolic delivery of mRNA, encoding for an antigen,
results in vaccine epitope synthesis of the transfected cells.
As a
result, mRNA therapeutics are easier to deliver as they do not have to cross
the nuclear membrane.
mRNA synthesis and purification are fast, easy and
low cost in comparision, even though mRNA is highly unstable under
physiological conditions.
Several strategies have been developed for RNA
delivery, including RNA conjugates, modified RNA, viral vectors, microparticles
and nanoparticles.
Viral vectors are the obvious choice for delivery, as
viruses have naturally evolved to become highly efficient at nucleic-acid
delivery.
Lipid nanoparticles
(LNPs) are among the most frequently used vectors for in vivo RNA
delivery.
In addition to ionizable cationic lipids, phospholipids,
cholesterol and lipid anchored polyethylene glycol (PEG) are the most commonly
used components for LNP formulations.
Lipids are
fatty acids insoluble in
water but soluble in organic
solvents.
Lipids come in four forms natural oils/fats, waxes,
phospholipids and steroids.
The theory of vesicle formation assumes that LNP formation is based on
disk-like bilayered fragments whose edges are stabilized by ethanol.
Phospholipids play a structural role in LNPs helping with
the formation and disruption of
the lipid bilayer to facilitate endosomal escape.
Furthermore, some
phospholipids possess polymorphic features and promote a transition from a
lamellar to a hexagonal phase in the endosome.
The properties of
individual LNPs strongly depend on local, microscopic mixing rates; diffusive
transport effects can lead to LNPs with variable compositions.
Early synthesis methods
relied on the formation of micrometer-sized vesicles by suspending lipids in
water, followed by sonication to produce submicrometer sized particles.
This top–down approach has many limitations, including molecular
degradation, contamination and lack of scalability.
Extrusion of a
lipid film through a small filter has been a popular synthesis method, often
used at the laboratory scale using syringe miniextruders.
Other
synthesis methods include the condensation of a lipid ethanol solution by rapid
injection into a vigorously stirred aqueous buffer.
Newer synthesis
methods directly mix the lipid–ethanol phase with an aqueous solution of
mRNA in a small T-piece; flow, mixing rates, controlled by pumps.
In
this way, LNPs with diameters of 70 nm or larger and high encapsulation
efficiencies can be generated.
Decorating the LNPs with immune cell
receptors may facilitate the uptake by the desired type of immune
cells.
The most important targets for mRNA
vaccines are antigen presenting cells (APCs), with dendritic cells (DCs) likely
being the most relevant cell type.
APCs are concentrated at high density
in lymph nodes (LNs).
The theory
is transfected DCs express the mRNA-encoded antigen.
The antigens are
subsequently processed by the proteasome, and the generated peptide epitopes
enter the endoplasmic reticulum where they are loaded onto major
histocompatibility complex (MHC) class I molecules.
The MHC class I
molecules are transported to the surface of the cell where the epitopes are
presented to CD8 T cells along with costimulatory signals.
Resence of
antigen fragments on MHC II induces antigen-specific antibodies.
There
is a pathway for the presentation of protein antigens on MHCI, not yet fully
understood, often too weak to elicit a potent cytotoxic immune
response.
Aluminum salts, used to enhance the immune response of
traditional vaccines, thought to be related to the effect of prolonged antigen
exposure, is still not understood in detail.
Including adjuvants with
the LNPs provides a way to further increase the potency of the vaccine and
guide the immune response in the desired direction.
In order to mount a
strong adaptive immune response, a vaccine needs to reach the LNs, where T-cell
activation and proliferation occurs.
Affinity maturation and isotype
switching of antibodies takes place in germinal centers in the
LNs.
Intradermal (ID) injection delivers LNPs directly into the skin, an
organ which is densely populated with Langerhans cells in the epidermis and
with multiple DC subtypes in the dermis.
The ID route of administration
has been shown to effectively induce a Th1 type immune response and cytotoxic
T-cell induction for mRNA–LNP vaccines.
IV injections of
LNP–mRNA vaccines are less common because of the potential of systemic
side effects.
Injecting immunogenic
material in the blood stream may lead to massive cytokine production, a
cytokine storm, that can lead to shock and
death.
The thickness of
polyethylene
glycol (PEG) coating on the LNPs is critical.
Coating the particles
with a lipid-anchored PEG containing lipid can reduce complement
activation.
PEG coating strongly influences the properties of the LNPs
and has to be tailored carefully.
A higher PEG content usually
increases the blood circulation time of LNPs, while reducing cellular uptake
and interaction with the endosomal membrane.
The surface of an LNP may
be decorated with specific targeting sequences which help with homing and
subsequent uptake.
Self-amplifying mRNA has been used to prolong protein
expression and to increase the immunogenicity of mRNA vaccines, which leads to
a dramatic decrease in the effective dose compared with nonreplicating
mRNA.
Self-amplifying mRNAs, also termed
replicons, are based on RNA viruses where the
structural viral proteins are replaced
with suitable mRNA encoding antigens, as well as with
RNA polymerases for
RNA replication.
The most studied replicons are derived from alphavirus
and flaviviruses.
When introduced into the cytosol of cells, the mRNA
will express the heterologous genes and replicate.
Through mRNA
amplification, large
amounts of desired antigens can be synthesized, accounting for up to 20% of
total cell protein.
Optimization of Lipid Nanoparticles for Intramuscular
Administration of mRNA Vaccines
We should not be surprised at
Rockefeller's hand in this as John D. Rockerfeller's father made his fortune
selling "patent" medicine.
William Avery "Bill" Rockefeller, Sr.
(November 13, 1810 – May 11, 1906) was
an American confidence
man who went by the alias of Dr. William Levingston.
He worked as a
traveling salesman who identified himself as a "botanic physician" and sold
elixirs.
His sons,
John Davison Rockefeller (July 8,
1839 – May 23, 1937) and William Avery
Rockefeller, Jr. (May 31, 1841 – June 24, 1922), were
Standard Oil
co-founders.
Several systems for
induction of transgene expression in
plants have been described recently.
Inducible systems were used mainly
in tobacco, rice,
Arabidopsis, tomato, and corn.
Inducible
systems offer researchers the possibility to deregulate gene expression levels
at particular stages of plant development and in particular tissues of
interest.
The more precise temporal and spatial control, obtained by
providing the transgenic plant with the appropriate chemical compound or
treatment, permits analysis of the function of those genes required for plant
viability.
Specific mutation of a gene can be achieved by a two-step
process.
Introduction of loxP sites around a functionally essential
genomic part followed by a cell type-specific Cre recombinase-mediated excision
of the loxP flanked sequence.
The same strategy can be used for cell
type-specific overexpression of a transgene, when a strong overall expressing
promoter is separated from the coding region of a gene of interest by loxP
flanked 'STOP' sequences.
In both scenarios, a Cre recombinase
transgene provides spatial control.
Once Cre expression
has been switched on and recombination has occurred, the resultant change in
gene expression is, in most cases, irreversible.
In the quest for the
development of pharmacological switches that control gene expression, no system
has been reported that regulates at the translational level but several systems
have been constructed:
-Tetracycline-inducible transgenic systems
[tetracycline transactivator (tTA) or 'Tet-Off' and reverse tetracycline
transactivator (rtTA) or 'Tet-On'] allow for reversible temporal regulation of
transgene expression .
Between these, rtTA is better suited for rapid
induction of gene expression.
-To permit small-molecule control of
transgene translation a farnesyl transferase inhibitor-responsive translation
initiation factor was constructed.
This
artificial
protein is a three-component chimaera consisting of the ribosome
recruitment core of the eIF4G1 eukaryotic translation initiation factor, the
RNA-binding domain of the R17 bacteriophage coat protein and the plasma
membrane localization CAAX motif of farnesylated H-Ras.
This
membrane-delocalized translation factor is inactive unless liberated in the
cytosol.
Farnesyl transferase inhibitor FTI-277 prevents the membrane
association of the CAAX motif and thus increases the cytoplasmic levels of the
eIF4G fusion protein, which is then capable of inducing translation of the
second cistron of a bicistronic messenger RNA containing an R17-binding site in
its intercistronic space.
- The concept of cisgenesis could become a
promising approach in future apple breeding.
However, cisgenesis
depends on the availability of effective tools for the
production of marker-free
genetically modified plants.
The development of such plants was recently
shown to be possible using a heat shock inducible Flp/FRT recombinase based
transformation system allowing the excision of the marker gene from the genome
of genetically modified apple plant tissue.
- A new laser mediated
method heat shocks
groups of cells allowing precise spatio-temporal control of gene expression
without requiring knowledge of specific enhancer sequences.
-The
baculovirus Autographa californica nucleopolyhedrovirus (AcNPV) has been widely
used to achieve a high level of foreign gene expression in insect cells, as
well as for efficient gene transduction into mammalian cells without any
replication.
In addition to permitting efficient gene
delivery, baculovirus has been shown to induce host innate immune responses in
various mammalian cells and in mice.
The major barrier to the clinical application of adenovirus gene
therapy for diseases that require stable transgene expression is the
immunogenicity of recombinant adenovirus, which ordinarily limits the duration
of its effects to a period of about 2 weeks.
If
tolerance to adenovirus
could be induced then transgene expression could be prolonged if
T lymphocytes underwent
thymic selection in the presence of adenovirus antigens.
The ability to
achieve unresponsiveness to a recombinant adenovirus after inoculation of the
thymus in neonates extends the
paradigm of intrathymic tolerance induction.
T lymphocytes are exquisitely
poised to respond rapidly to pathogens and have proved
an instructive model for
exploring the regulation of inducible genes.
Individual genes respond
to antigenic stimulation in different ways, and it has become clear that the
interplay between transcription factors and the chromatin platform of
individual genes governs these
responses.
Understanding of the
complexity of the chromatin platform and the
epigenetic
mechanisms that contribute to transcriptional control has expanded
dramatically in recent years.
These mechanisms include the
presence/absence of histone modification marks, which form an epigenetic
signature to mark active or inactive genes.
These signatures are
dynamically added or removed by epigenetic enzymes, comprising an array of
histone-modifying enzymes, including the more recently recognized
chromatin-associated signalling kinases.
In addition,
chromatin-remodelling complexes physically alter the chromatin structure to
regulate chromatin accessibility to transcriptional regulatory factors.
The advent of genome-wide technologies has enabled characterization of
the chromatin landscape of T lymphocytes
in terms of histone occupancy, histone modification patterns and transcription
factor association with specific genomic regulatory regions, generating an
image of the T lymphocyte epigenome.
The use of transgenic
animals in the field of molecular genetics is standard and neccesary for
control purposes.
Molecular genetics experiments use only model
organisms with known regulatory DNA sequences, i.e. enhancers, that drive gene
expression at particular times in development and in particular cells.
By reducing the variables
it becomes easier to predict mutational effects with transgenic animals.
It is impossible to
predict how these genetic switches would function in animals outside of those
specifically bred for the purposes of these experiments.
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