Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Bacteriophage vectors
Bacteriophage
WHY BACTERIOPHAGE AS A VECTOR?
M13 phage
Genome of m13 phage
Life cycle and dna replication of m13
CONSTRUCTION M13 AS PHAGE VECTOR
M13 MP 2 vector
M13MP7 VECTOR
Selection of recombinants
Lambda replacement vectors
LAMBDA EMBL 4 VECTOR
P1 PHAGE
GENOME OF P1 PHAGE
P1 PHAGE AS VECTOR
P1 phage vector system
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Bacteriophage vectors
Bacteriophage
WHY BACTERIOPHAGE AS A VECTOR?
M13 phage
Genome of m13 phage
Life cycle and dna replication of m13
CONSTRUCTION M13 AS PHAGE VECTOR
M13 MP 2 vector
M13MP7 VECTOR
Selection of recombinants
Lambda replacement vectors
LAMBDA EMBL 4 VECTOR
P1 PHAGE
GENOME OF P1 PHAGE
P1 PHAGE AS VECTOR
P1 phage vector system
Restriction Endonuclease: The Molecular Scissor of DNA - By RIKI NATHRIKI NATH
restriction enducleases are called the molecular scissors of DNA. types of restriction enzymes, their structures, subunits, most importantly the use of Type II restriction endonuclease in recombinant technology, mechanism of enzyme action and their applications.
Interplay between Metabolism and EpigeneticsAbhishek M
This ppt gives you an idea about the inter-connections between epigenetics and metabolism. How nutrition affects epigenetics and how epigenetic changes may cause metabolic disorders.
Here is an introduction to the renal mechanisms of clearance and pH balance with some slides dedicated to the differences between metabolic and respiratory acidosis and alkalosis.
Please point out any mistakes or omissions, it'll really be appreciated.
Here is some information about 5 important immunological techniques including Flowcytometry and RIA
I hope it helps and please comment if u come across any mistakes or scope for improvement, it'll really be appreciated.
A brief introduction to two techniques used to study protein interactions: Yeast two hybrid (Y2H) system and Chromatin immunoprecipitation(ChIP)
I hope it helps and please comment if I've made any mistakes.
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.
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
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.
2. 2
What are restriction enzymes?
●
Molecular scissors that cuts DNA.
●
Identifies specific Recognition sites.
●
Found naturally in prokaryotes as a defence
mechanism.
●
Do not cut host DNA- But how?
●
A useful tool in DNA modification and
manipulation.
3. 3
BRIEF HISTORY
Year Significant Event Scientists Involved
1950s Host controlled restriction
and modification
Luria, Weigle and Bertani
1960s
Restriction caused by
enzymatic cleavage of
phage DNA
Arber and Meselson
1970
Type II restriction
enzyme(RE) discovered
Smith, Kelly and Wilcox
1970s Use in DNA Mapping Nathans and Danna
1978 Nobel Prize for Physiology
or Medicine
Werner Arber, Daniel
Nathans, and Hamilton
Smith.
4. 4
RESTRICTION SYSTEM
●
REs scan the length of DNA.
●
It identifies specific sequences.
●
Binds to DNA at restriction site.
●
Makes a cut in the sugar-phosphate backbone.
●
Mg2+ acts as a co-factor in this process.
●
Blunt or staggered end cuts are formed.
5. 5
MODIFICATION SYSTEM
●
The sequence specific methylation of host DNA
is called as modification.
●
Restriction functions only on unmethylated host
DNA.
●
This is what protects the host from its own REs.
●
Modification is done by the methyltransferase
domain of the REs.
6. 6
NOMENCLATURE
●
First letter derived from genus.
●
Next two comes from the specific species.
●
Next letter is the name of the strain.
●
The final letter tells you the order of identification
of the enzyme in the bacteria.
●
Eg: EcoRI, HindIII, BamHI etc.
7. 7
Types of Restriction Enzymes
Type of RE Type I Type II Type III Type IV
Features Oligomeric
REase and
MTase complex.
Require ATP
hydrolysis for
restriction.
Cleave variably,
often far from
recognition site
Separate REase
and MTase or
combined
REase MTase∼MTase
fusion.
Cleave within or
at fixed
positions close
to recognition
site.
Combined
REase + MTase
complex.
ATP required for
restriction.
Cleave at fixed
position outside
recognition site.
Methylation-
dependent
Rease.
Cleave at
variable distance
from recognition
site.
Cleave m6A,
m5C, hm5C
and/or other
modified DNA.
Genes hsdR, hsdM,
hsdS
ecorIR, ecorIM ecoP1IM,
ecoP1IR
mcrA, mcrBC,
mrr
Examples EcoK1 EcoR1 EcoP1I No typical
examples
8. 8
FUNCTIONAL ROLES OF R-M SYSTEM
●
,
S MT
ET M
SEQUENCE SPECIFICITY METHYL TRANSFERASE
TRANSLOCATION SAM-BINDING ENDONUCLEASE
9. 9
TYPE I ENDONUCLEASES
●
First to be identified by Arber and Meselson.
●
Asymmetric recognition sequence.
●
Requires various co-factors including SAM, ATP and Mg2+.
●
Single enzyme that performs restriction and modification
functions.
●
Contains 3 subunits HsdS, HsdM and HsdR.
10. 10
TYPE III ENDONUCLEASES
●
Cleave DNA at immediate vicinity, about 20-30 base pairs away
from recognition sequence.
●
Recognises two separate non-pallindromic sequences that are
inversely oriented.
●
ATP, SAM (not essential) and Mg2+ acts as co-factor.
●
Separate enzymes for restriction and modification, but share a
common subunit.
11. 11
TYPE II ENDONUCLEASES
●
First identified in 1970 (HindII).
●
Most commonly used in genetic manipulation experiments.
●
Recognizes 4-8 bp long pallindromic sequences.
●
Cleaves within (mostly) the recognition sequence.
●
Only Mg2+ required as cofactor, doesn’t require SAM or ATP for
function.
12. 12
How Type II Res work?
FIGURE: Mechanism of type II RE action
SOURCE: Pingoud and Jeltsch, 2001
13. 13
Applications of Type II REs
●
Gene cloning and protein expression experiments.
●
Restriction mapping and vector designing.
●
Study fragment length differences among
individuals. Eg: RFLP, AFLP.
14. 14
Previous Years Entrance Questions
Question 1: Which one of the following marker types uses
combination of both restriction enzymes and PCR
techniques? (CSIR-NET: June 2014, Part-B)
●
SSR
●
AFLP
●
SNP
●
RAPD
20. 20
REFERENCES:
●
Horton, J. et al. (2006). Structure and substrate recognition of the Escherichia coli DNA
adenine methyltransferase. Journal of Molecular Biology, 358, 559–570.
●
Kennaway, C. et al. (2012). Structure and operation of the DNA-translocating type I DNA
restriction enzymes. Genes Development, 26(1), 92-104.
●
Leonen, W. et al. (2014). Highlights of the DNA cutters: a short history of the restriction
enzymes. Nucleic acids research, 42(1), 3-19.
●
Pingoud, A. and Jeltsch, A. (2001). Structure and function of type II restriction endonucleases.
Nucleic acids research, 29(18), 3705-3727.
●
Pingoud, A. et al. (2014). Type II restriction endonucleases:a historical perspective and more.
Nucleic acids research, 42(12), 7489-7527.
●
Roberts, R. (2005). How restriction enzymes became the workhorses of molecular biology.
Proceedings of the National Academy of Sciences of the United States of America, 102(17),
5905-5908.
●
Toliusis, P. (2017). CgII cleaves DNA using a mechanism distinct from other ATP-dependent
restriction endonucleases. Nucleic acids research, 45(14), 8435-8447.
