Gene silencing is a molecular process that down regulates gene expression at the transcriptional or translational level. It allows researchers to study essential genes and provides insight into disease development since many diseases are associated with reduced gene expression. Gene silencing occurs through various mechanisms including histone modification, DNA methylation, and small RNA pathways. It has applications in research areas like producing virus resistant plants and modifying food quality and plant traits.
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
RNA interference (RNAi): Cellular process by which an mRNA is targeted for degradation by a dsRNA with a strand complementary to a fragment of such mRNA.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
RAPD markers are decamer DNA fragments.
RAPD is a type of PCR reaction.
as the name suggest it is a fast method when compared to the traditional PCR medthod.
RNA interference (RNAi): Cellular process by which an mRNA is targeted for degradation by a dsRNA with a strand complementary to a fragment of such mRNA.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication.
What is Genome,Genome mapping,types of Genome mapping,linkage or genetic mapping,Physical mapping,Somatic cell hybridization
Radiation hybridization ,Fish( =fluorescence in - situ hybridization),Types of probes for FISH,applications,Molecular markers,Rflp(= Restriction fragment length polymorphism),RFLPs may have the following Applications;Advantages of rflp,disAdvantages of rflp, Rapd(=Random amplification of polymorphic DNA),Process of rapd, Difference between rflp &rapd
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
2. • defined as a molecular process involved in the down
regulation of specific genes.
• Interruption or suppression of the expression of a gene at transcriptional or translational
levels.
• “switching off”
• Gene silencing is same as gene knock down but is totally different from gene knock out.
• When genes are knock down ,there expression is reduced by at least 70% , where in
contrast when genes are knocked out, they are completely eliminate from organism’s
genome.
• allow researchers to study essential genes that are required for the animal models to
survive and cannot be removed.
• they provide a more complete view on the development of diseases since diseases are
generally associated with genes that have a reduced expression.
• probably evolved as a genetic defense system against viruses and invading nucleic acids
(Brigneti et al., 1998; Voinnet et al., 2000; Waterhouse et al., 2001; Wassenegger, 2002)
5. Silencing is a position effect---a gene is
silenced because of where it is located, not
in response to a specific environmental signal.
Also, silencing can “spread” over large
stretches of DNA ,switching off multiple
genes, even ones quite distant from the
initiating event.
The most common form of silencing is
associated with a dense form of chromatin
called heterochromatin.
Both activation and repression of
transcription often involve modification of
nucleosomes to alter the accessibility of a
gene to the transcriptional machinery and
other regulatory proteins.
Transcription can also be silence by
methylation of DNA by enzymes called DNA
methylases.
6.
7. Rap1 recruits SIR complex to the telomere.
SIR2, a component of that complex, deacetylates nearby nucleosomes.
The unacetylated tails themselves then bind Sir3 and SIR4, recruiting
more SIR complex, allowing the SIR2 within it to act on
nucleosomes further away, and so on.
This explains the spreading of the silencing effect produced by deacetylation.
The telomeres, the silent mating-type locus, and the rDNA genes are all “silent” regions in
Saccharomyces cerevisiae.
Silencing in Yeast Is Mediated by Deacetylation and
Methylation of Histones.
8. Consider the telomere as an example.
•The final 1-5 kb of each chromosome is found in a folded , dense
structure.
•Genes taken from other chromosomal locations and moved to this
region are
often silenced, particularly if they are only weakly expressed in
their usual location.
•Mutations have been done , in which a gene placed at the telomere
is expressed at higher levels.
•These studies implicate three genes encoding regulators of
silencing:
Silent information regulator(SIR)2,3 and 4.
The three proteins encoded by these genes form a complex that
associates with silent chromatin, and Sir2 is a histone deacetylase.
•The silencing complex is recruited to the telomere by a DNA-
binding protein(RAP1) that recognizes the telomere’s repeated
sequences.
•Histone methyl transferases attach methyl groups to histone tails.
•Just as acetylated residues within histones are recognized by
proteins bearing bromodomains, methylated residues bind proteins
with chromodomains.
9. Position effect
• Position effect is the effect
on the expression of a
gene when its location in a
chromosome is changed,
often by translocation.
• described in Drosophila
with respect to eye colour
and is known as
position effect variegation
(PEV).
10.
11. Repression by polycomb also uses histone methylation
Polycomb repressive complex 1
Polycomb Response Elements (PREs)
DNA binding subunit (PHO or PHOL - Repressive Complex )
Polycomb protein (PHO) = Protein pleiohomeotic
12. Switching a gene off through DNA methylation
and histone midification
13. DNA Methylation Is Associated
with Silenced Genes in Mammalian Cells
Some mammalian genes are kept silent by methylation of nearby DNA sequences.
Methylation of DNA can mark sites where heterochromatin subsequently forms.
DNA methylation lies at the heart of a phenomenon called imprinting.
Two regulatory sequences are critical for the differential expression of the human
H19 and Igf2 genes:
An enhancer and an insulator.
14. Imprinting
Two examples of genes controlled by imprinting- the mammalian Igf2 and H19 genes.
The H19 genes is expressed from only the matermal chromosome, Igf2 from the paternal
chromosome.
The methylation state of the insulator element determines whether or not the insulator binding
protein( CTCF) can bind and block activation of the H19 gene from the downstream enhancer.
15. Some States of Gene Expression Are
Inherited through Cell Division even when
the Initiating Signal Is No Longer Present
Patterns of DNA methylation can be maintained
through cell division
17. Paramutation :
• In epigenetics, a paramutation is an
interaction between two alleles at a single
locus, whereby one allele induces a heritable
change in the other allele.
• The change may be in the pattern of DNA
methylation or histone modifications.
• For example – Anthocyanin pigment in corn
plant
• B allele – Anthocyanin pigment coded
• Paramutagenic allele at this locus(B’) cause
reduced pigment production
• B allele is silenced by the B’ allele in the first
generation
• In next generation, the newly silence B allele is
paramutagenic and silence.
18. Transposon
silencing:
• is a product of histone
modification that prevent
the transcription of that
area of DNA.
• The “jumping” of
transposon generates the
genomic instability and
cause the extremely
deleterious mutations.
19. Transgene silencing:
• insertion of transgene in to a
transcriptionally inactive part
of genome.
When an insertion of any
transgene it does not show
activity as per desire and this is
because of it’s instability.
• The lose of transgene stability is
because of gene silencing.
• E.g. slow fruit softening tomato,
by reducing expression of
polygalactouronase enzyme.
20. RNA Directed DNA
Methylation:
• an epigenetic process
first elucidated in plants
where by small double-
stranded RNAs (dsRNA's)
are processed to guide
methylation to
complementary DNA
loci.
• In Arabidopsis thaliana
23. RNA i
(RNA interference):
• it is a post
transcriptional process
triggered by the
introduction of double
stranded RNA (ds RNA)
which leads to the gene
silencing in a sequence
specific manner.
• It is also known as post
transcriptional gene
silencing / co
suppression and
quelling.
24.
25.
26. Non sense
Mediated Decay:
• is a cellular mechanism
of mRNA surveillance
that functions to detect
nonsense mutations and
prevent the expression
of truncated or
erroneous proteins.
• NMD is triggered by
exon junction complexes
(EJCs) (components of
the assembled RNP) that
are deposited during pre-
mRNA processing.
27. Anti sense RNA
technology:
• It blocks the activity of the
mRNA in a stoichiometric
manner.
• Antisense RNA has the opposite
sense to m RNA.
• The presence of complimentary
sense and antisense RNA in the
in the same cell can lead to the
formation of a stable duplex
which interferes with gene
expression at the level of RNA
processing or possible
translation.
• This technology widely used in
plants for gene inhibition.
30. GENE SILENCING IN PLANTS
Currently, there are several routes of GS identified in plants, such as:
• transcriptional gene silencing (Vaucheret & Fagard, 2001),
• post-transcriptional gene silencing or RNA interference (PTGS or
RNAi) (Vaucheret et al., 2001),
• microRNA silencing (Bartel, 2004),
• and virus induced gene silencing (Burch-Smith et al., 2004).
• All these pathways play an important role at the cellular level,
affecting differentiation, gene regulation (Bartel, 2004), and
protection against viruses and transposons (Waterhouse et al.,
2001).
31.
32.
33. Applications for GS in plants
• the production of virus resistant plants through genetic
transformation.
• used in food quality modification such as the reduction of
caffeine levels in coffee beans and to increase the
nutritional value of corn protein and tomato.
• Research on forest tree yield and quality has included the
study of GS related to lignin synthesis.
• research on fruit crops has targeted applications of GS on
viral and bacterial resistance, and physiological aspects
such as self fertility.
34. Advantages of gene silencing:
• Downregulation of gene expression simplifies "knockout" analysis.
• Easier than use of antisense oligonucleotides. Si RNA more effective and sensitive at lower concentration.
• Cost effective
• Can be labelled Ease of transfection by use of vector
• blocking expression of unwanted genes and undesirable substances.
• Inducing viral resistance
• Powerful tool for analysing unknown genes in sequenced genomes.
• Useful approach in future gene therapy.
• Oligonucleotides can be manufactured quickly, some within one week; the sequence of the mRNA is all that is
needed.
• Cancer treatments
• Modulation of HIV-I replication by RNA i.
• Small RNA and it’s application in andrology and urology.
35. Disadvantages of gene silencing:
• ”High pressure injection” and electroporation can cause significant
damage to the integrity of the normal tissues and organs and thus
preclude the utilisation in a clinical set-up.
• Liposomes/cationic encapsulated Si RNA may also be toxic to the
host and may cause severe host immune responses.
• Other emerging strategies includes chemical modification of Si RNA
molecules and encapsulated with different molecules are still in
their infancy and need to be thoroughly investigated before used in
therapeutic applications.