The document discusses gene expression and transcription. It begins by outlining the central dogma of biology, where DNA is transcribed into RNA which is then translated into protein. It then describes the regulation of transcription in eukaryotes and prokaryotes. In eukaryotes, transcription factors bind to specific DNA sequences to activate or repress transcription. Histone acetylation also regulates transcription by altering chromatin structure. The three eukaryotic RNA polymerases are described along with initiation, elongation, termination and processing of transcripts. Transcription in prokaryotes similarly involves RNA polymerase binding to promoter sequences with sigma factors and termination via Rho-dependent and independent mechanisms.
This presentation explains the fundamentals of Genetic Code, Protein synthesis mechanism and Antibiotics that inhibits at various stages of Translation.
This Powerpoint consists of RNA synthesis (transcription) in prokaryotes and eukaryotes. This also explains about the post-transcriptional modifications in the mRNA. How the post transcriptionla modifications help in the gene expression.
The flow of information in the cell starts at DNA, which replicates to form more DNA. Information is then ‘transcribed” into RNA, and then it is “translated” into protein.
Information does not flow in the other direction.
A few exceptions to the Central Dogma exist
some RNA viruses, called “retroviruses”.
Gene regulation, History and Evolution , Traditional Methods:
Northern blot
quantitative reverse transcription PCR (qRTPCR)
serial analysis of gene expression(SAGE) and
DNA microarrays.
DNA Chip
This presentation explains the fundamentals of Genetic Code, Protein synthesis mechanism and Antibiotics that inhibits at various stages of Translation.
This Powerpoint consists of RNA synthesis (transcription) in prokaryotes and eukaryotes. This also explains about the post-transcriptional modifications in the mRNA. How the post transcriptionla modifications help in the gene expression.
The flow of information in the cell starts at DNA, which replicates to form more DNA. Information is then ‘transcribed” into RNA, and then it is “translated” into protein.
Information does not flow in the other direction.
A few exceptions to the Central Dogma exist
some RNA viruses, called “retroviruses”.
Gene regulation, History and Evolution , Traditional Methods:
Northern blot
quantitative reverse transcription PCR (qRTPCR)
serial analysis of gene expression(SAGE) and
DNA microarrays.
DNA Chip
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
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.
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.
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.
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.
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/
Lateral Ventricles.pdf very easy good diagrams comprehensive
3 Gene expression.pdf
1. Gene expression
Mohammad Ridhuan Mohd Ali
Bacteriology Unit
Infectious Disease Research Centre (IDRC)
Institute for Medical Research (IMR), Malaysia
2. Central dogma
• first proposed in 1958
by Francis Crick
• the process by which
the instructions in
DNA are converted
into a functional
product
• DNA->RNA->protein
3. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
4. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
Activator
5. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
Activator Repressor
6. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
Activator Repressor
Enhancer
7. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
Activator Repressor
Enhancer Silencer
8. Regulation of transcription
• Transcription factor (TF)
• protein that regulate gene expression
• binding to specific sequences that are associated with a transcription
initiation site
Activator Repressor
Enhancer Silencer
11. Transcription in eukaryotes
• Involves three different enzymes:
• RNA pol. I
• located in the nucleolus
• catalysed the synthesis of all rRNAs except the small 5S rRNA.
• RNA pol. II
• transcribes nuclear genes that encode proteins and other proteins
• specifying hnRNAs (heterogenous nuclear RNAs).
• hnRNAs also known as pre-mRNA
• RNA pol. III – catalysed the synthesis of tRNAs, 5S rRNAs and snRNAs.
12. Transcription in eukaryotes
• All three RNA polymerase require the assistance of transcription factors (TF) to initiate the synthesis
of RNA chains.
• exhibit different sensitivities to α-amanitin, metabolic poison from mushroom Amanita phalloides
• α-amanitin can be used to determine which RNA polymerase catalyzes the transcription of a
particular gene.
13. Transcription in eukaryotes
• Initiation
• Eukaryotic RNA pol. requires transcription factors (TFs) to
initiate the RNA synthesis.
• TFs must bind to the promoter region in DNA and form a
complex, before RNA pol will bind and initiate transcription.
• Promoters recognized by RNA pol II has a short conserved
element, located upstream the transcription start point.
15. Transcription in eukaryotes
• Initiation
• begins ways before the transcription start point
• Requires an orchestra of RNA polymerase and transcription factors (TFs)
16. Transcription in eukaryotes
• Elongation
• Once the RNA polymerases has been released from the initiation complex,
the elongation process is the same as in prokaryotes.
• 7-methyl guanosine (MG) caps are added at the 5’ ends of pre-mRNA, shortly
after the elongation process begins (about 30 nucleotides long).
• 7-MG caps are recognized by factors involved initiation of translation
• Protect the growing RNA chains from nucleases.
17. • Termination
• The 3’-ends of the RNA transcripts
are produced by endonuclolytic
cleavage, rather than termination
of transcription.
• The actual termination occurs 1k-
2k nucleotides, downstream from
the 3’ end of mature transcripts
• Between AAUAAA andG-U rich
sequence
Transcription in eukaryotes
18. Transcription in eukaryotes
• After cleavage, the enzyme poly(A) polymerase adds poly(A) tails
about 200 nucleotides to the 3’ ends (polyadenylation).
• Poly A tails
• enhance the stability of the mRNAs
• play important role in their transport from nucleus to the cytoplasm.
20. Transcription in prokaryotes
• Initiation
• at specific promoters
• Prokaryote RNA polymerase
• Has 5 subunits of polypeptides
• ß’ – largest subunit
• ß – second largest
• αI – NTD assembly of RNAP
• αII – CTD bind to promoter
• Ω – assist, stabilise RNAP to bind to the promoter
21. Transcription in prokaryotes
• Initiation
• at specific promoters
• Prokaryote RNA polymerase
• Has 5 subunits of polypeptides
• ß’ – largest subunit
• ß – second largest
• αI – NTD assembly of RNAP
• αII – CTD bind to promoter
• ω – assist, stabilise RNAP to bind to the promoter
• Require σ factor to initiate the transcription
22. Transcription in prokaryotes
• Promoter sites
• The sequence vary from gene to gene, but some
are highly conserved; Consensus sequence
• The -10 consensus sequence in the non-
template strand is 5’-TATAAT-3’ (Pribnow box);
this A:T rich region facilitates the localized
unwinding of the DNA.
• The -35 consensus sequence is 5’-TTGACA-3’
(also called the recognition sequence, subunit
initially recognize and binds to this sequence).
• Distance between the two sequences is 15 -20
bp
26. Transcription in prokaryotes
• Termination
• Happen in two ways
• Rho independent
• Rho dependent
• Rho hexameric protein
27. Transcription in prokaryotes
• Termination
• Happen in two ways
• Rho independent
• Rho dependent
• Rho hexameric protein
• Rho Utilisation Site (Rut site) (Cystine-rich)
28. Transcription in prokaryotes
• Termination
• Happen in two ways
• Rho independent
• Rho dependent
• Rho hexameric protein
• Rho Utilisation Site (Rut site) (Cystine-rich)
• In prokaryotes, translation and degradation of an mRNA often begin before
termination
• mRNA molecules are synthesized, translated and degraded in the 5’ to 3’
direction,
• all three processes can occur simultaneously on the same RNA molecule.
29. Transcription in prokaryotes
• Termination
• Happen in two ways
• Rho independent
• Rho dependent
• Rho hexameric protein
• Rho Utilisation Site (Rut site) (Cystine-rich)
• In prokaryotes, translation and degradation of an mRNA often begin before
termination
• mRNA molecules are synthesized, translated and degraded in the 5’ to 3’
direction,
• all three processes can occur simultaneously on the same RNA molecule.
32. mRNA vaccine
Element Description Position
cap A modified 5’-cap1 structure (m7G+m3'-5'-ppp-5'-Am) 1-2
5’-UTR 5´-untranslated region derived from human alpha-globin RNA with an optimized Kozak
sequence
3-54
sig S glycoprotein signal peptide (extended leader sequence), which guides translocation of
the nascent polypeptide chain into the endoplasmic reticulum.
55-102
S protein_mut Codon-optimized sequence encoding full-length SARS-CoV-2 spike (S) glycoprotein
containing mutations K986P and V987P to ensure the S glycoprotein remains in an
antigenically optimal pre-fusion conformation; stop codons: 3874-3879 (underlined)
103-3879
3’-UTR The 3´ untranslated region comprises two sequence elements derived from the amino-
terminal enhancer of split (AES) mRNA and the mitochondrial encoded 12S ribosomal
RNA to confer RNA stability and high total protein expression.
3880-4174
poly(A) A 110-nucleotide poly(A)-tail consisting of a stretch of 30 adenosine residues, followed by
a 10-nucleotide linker sequence and another 70 adenosine residues.
4175-4284
