Cot curve dispersed repeated DNA or interspersed repeated DNA tandem repeated DNA Long interspersed repeat sequences (LINEs) Short interspersed nuclear elements (SINEs) satellite, minisatellite and microsatellite DNA Variable Number Tandem Repeat (or VNTR)
Sanger sequencing is one of the DNA sequencing methods used to identify and determine the sequence (Nucleotide) of DNA .This is an enzymatic method of sequencing developed by Fred Sanger.
Facts about DNA
Eukaryotic chromosomes
Chemical composition of eukaryotic chromosomes
Histones
Non-histone chromosomal protein
Scaffold proteins
Folded fibre model
Nucleosome model
H1 proteins
Histone modification
Chromatosome
Higher order of chromatin structure
Mechanism of DNA packaging
Conclusion
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
This Presentation will be helpful to undergraduate and postgraduate students of biology and biotechnology in understanding the significance of COT curves in determination of gene and genome complexity amoug various organisms
Sanger sequencing is one of the DNA sequencing methods used to identify and determine the sequence (Nucleotide) of DNA .This is an enzymatic method of sequencing developed by Fred Sanger.
Facts about DNA
Eukaryotic chromosomes
Chemical composition of eukaryotic chromosomes
Histones
Non-histone chromosomal protein
Scaffold proteins
Folded fibre model
Nucleosome model
H1 proteins
Histone modification
Chromatosome
Higher order of chromatin structure
Mechanism of DNA packaging
Conclusion
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
This Presentation will be helpful to undergraduate and postgraduate students of biology and biotechnology in understanding the significance of COT curves in determination of gene and genome complexity amoug various organisms
genome structure and repetitive sequence.pdfNetHelix
Welcome to our channel, where science meets discovery! In today's enlightening video, we unravel the mysteries of life at its most fundamental level - the chromosomes.
Join us on an exhilarating journey deep within the human cell as we explore the intricate architecture and organization of these tiny yet immensely powerful structures.
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Safalta Digital marketing institute in Noida, provide complete applications that encompass a huge range of virtual advertising and marketing additives, which includes search engine optimization, virtual communication advertising, pay-per-click on marketing, content material advertising, internet analytics, and greater. These university courses are designed for students who possess a comprehensive understanding of virtual marketing strategies and attributes.Safalta Digital Marketing Institute in Noida is a first choice for young individuals or students who are looking to start their careers in the field of digital advertising. The institute gives specialized courses designed and certification.
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Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
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Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
4. Analysis of DNA Sequences in
Eukaryotic Genomes
• The technique that is used to determine the sequence
complexity of any genome involves the denaturation and
renaturation of DNA.
• DNA is denatured by heating which melts the H-bonds and
renders the DNA single-stranded.
• If the DNA is rapidly cooled, the DNA remains single-stranded.
• But if the DNA is allowed to cool slowly, sequences that are
complementary will find each other and eventually base pair
again.
• The rate at which the DNA reanneals is a function of the
species from which the DNA was isolated.
5. • The Y-axis is the percent of the DNA that remains
single stranded.
• This is expressed as a ratio of the concentration
of single-stranded DNA (C) to the total
concentration of the starting DNA (Co).
• The X-axis is a log-scale of the product of the
initial concentration of DNA (in moles/liter)
multiplied by length of time the reaction
proceeded (in seconds).
• The designation for this value is Cot and is called
the "Cot" value.
• The curve itself is called a "Cot" curve.
6. • As can be seen the curve is rather smooth
which indicates that reannealing occurs
slowing but gradually over a period of time.
• One particular value that is useful is Cot½ , the
Cot value where half of the DNA has
reannealed.
• The shape of a "Cot" curve for a given species
is a function of two factors:
– the size or complexity of the genome; and
– the amount of repetitive DNA within the genome
7.
8. Reassociation kinetics
• A sample with a highly-repetitive sequence
will renature rapidly, while complex
sequences will renature slowly
• The Amount of renaturation is measured
relative to a C0t value.
• The C0t value is the product of C0 (the initial
concentration of DNA), t (time in seconds),
and a constant that depends on the
concentration of cations in the buffer.
• Repetitive DNA will renature at low C0t
values, while complex and unique DNA
sequences will renature at high C0t values.
9. • The larger the genome size the longer it will take for any one
sequence to encounter its complementary sequence in the
solution.
• This is because two complementary sequences must
encounter each other before they can pair.
• The more complex the genome, that is the more unique
sequences that are available, the longer it will take for any
two complementary sequences to encounter each other and
pair.
• Given similar concentrations in solution, it will then take a
more complex species longer to reach Cot½ .
10.
11.
12. Repetitive DNA Sequences
• Repeated DNA sequences are DNA sequences
that are found more than once in the
genome of the species, have distinctive
effects on "Cot" curves.
• If a specific sequence is represented twice in
the genome it will have two complementary
sequences to pair with and as such will have a
Cot value half as large as a sequence
represented only once in the genome.
13. • Genomes that contain these different
classes of sequences reanneal in a
different manner than genomes with
only single copy sequences.
• Instead of having a single smooth "Cot"
curve, three distinct curves can be
seen, each representing a different
repetition class.
• The first sequences to reanneal are the
highly repetitive sequences because so
many copies of them exist in the
genome, and because they have a low
sequence complexity.
• The second portion of the genome to
reanneal is the middle repetitive DNA,
and the final portion to reanneal is the
single copy DNA or unique DNA
sequence.
14. Single copy sequences are found once
or a few times in the genome.
• Unique or non-repetitive sequences are those
found once or a few times within the genome.
• Structural genes are typically unique sequences of
DNA.
• The vast majority of proteins in eukaryotic cells are
encoded by genes present in one or a few copies.
• In humans, unique sequences are estimated to make
up approximately 55–60% of the genome.
15. Some moderately repetitive
sequences are transcribed
• Moderately repetitive DNA present in a few
to about 105
copies in the genome.
• Middle repetitive DNA can vary from 100-
300bp to 5000 bp and can be dispersed
throughout the genome.
• In a few cases, moderately repetitive
sequences are multiple copies of the same
gene.
16. • For example, the genes that encode ribosomal RNA
(rRNA) are found in many copies.
– Ribosomal RNA is necessary for the functioning of
ribosomes. Cells need a large amount of rRNA for making
ribosomes, and this is accomplished by having multiple
copies of the genes that encode rRNA.
• Likewise, the histone genes are also found in
multiple copies because a large number of histone
proteins are needed for the structure of chromatin.
• In addition, other types of functionally important
sequences can be moderately repetitive
17. Highly repetitive sequences are
present in large numbers of copies
• The most abundant sequences are found in the
highly repetitive DNA class.
• Highly repetitive DNA present in about 105
to
107
copies in the genome and can range in size
from a few to several hundred bases in length.
• These sequences are found in regions of the
chromosome such as heterochromatin,
centromeres and telomeres and tend to be
arranged as a tandem repeats.
18. Species Sequence Distribution
Bacteria 99.7% Single Copy
Mouse
60% Single Copy
25% Middle Repetitive
10% Highly Repetitive
Human
70% Single Copy
13% Middle Repetitive
8% Highly Repetitive
Cotton
61% Single Copy
27% Middle Repetitive
8% Highly Repetitive
Corn
30% Single Copy
40% Middle Repetitive
20% Highly Repetitive
Wheat
10% Single Copy
83% Middle Repetitive
4% Highly Repetitive
Arabidopsis
55% Single Copy
27% Middle Repetitive
10% Highly Repetitive
19. Repetitive-Sequence DNA.
• Both moderately repetitive and highly
repetitive DNA sequences are sequences that
appear many times within a genome.
• These sequences can be arranged within the
genome in one of two ways:
– distributed at irregular intervals—known as
dispersed repeated DNA or interspersed repeated
DNA
– or clustered together so that the sequence
repeats many times in a row—known as tandemly
repeated DNA.
25. Interspersed genome-wide repeats
• Dispersed repeated sequences consist of families of
repeated sequences interspersed throughout the
genome.
• They can be either short or long and many have the
added distinction of being either an actual mobile
elements (transposons or retrotransposons) or
sequences derived from mobile elements.
• Transposons are mobile DNA sequences which
migrate to different regions of the genome via
transposition.
26. Interspersed genome-wide repeats
• A large portion of portion of eukaryotic genomes are
composed of such sequences.
• They fall into several classes, and together they can
form a substantial part of the genome about 45% or
more in humans and 50% in maize.
• Most dispersed, repeated sequences correspond to
the category of middle repetitive DNA, the number
of copies varying between a few and a few thousand.
27. • Two types of dispersed repeated sequences
are known:
– Long interspersed elements (LINEs), in which the
sequences in the families are about 1,000–
7,000bp long; and
– Short interspersed elements (SINEs), in which the
sequences in the families are 100–400 bp long.
28. • All eukaryotic organisms have LINEs and
SINEs, with a wide variation in their relative
proportions.
• Humans and frogs, for example, have mostly
SINEs, whereas Drosophila and birds have
mostly LINEs.
• LINEs and SINEs represent a significant
proportion of all the moderately repetitive
DNA in thegenome
29. Long interspersed repeat sequences (LINEs)
• Long interspersed repeat sequences (LINEs)
are mammalian retrotransposons that in
contrast to retroviruses lack long terminal
repeats (LTRs).
• LINEs (long interspersed nuclear elements),
comprise about 21% of the human genome.
and consist of repetitive sequences up to 6500
bp long that are adenine-rich at their 3’ends.
30. • Mammalian diploid genomes have about
500,000 copies of the LINE-1 (L1) family,
representing about 21% of the genome.
• Other LINE families may be present also, but
they are much less abundant than LINE-1.
Fulllength LINE-1 family members are 6–7 kb
long, although most are truncated elements of
about 1–2 kb.
31. • LINEs encode two open reading frames (ORF1 and 2),
which are translated.
• LINE1 (L1) element is about 6.1kb long and encode
two open reading frames (ORF1 {1kb} and 2 {4kb} )
– RNA-binding protein p40 and
– a protein with both endonuclease and reverse transcriptase activities.
• At the 5’ end and at the 3 end they have an
untranslated region (5’ UTR and 3’UTR).
32. • The 5' UTR contains the promoter sequence,
while the 3' UTR contains a polyadenylation
signal (AATAAA) and a poly-A tail.
• Approximately 600000 L1 elements are
dispersed throughout the human genome.
• This can result in genetic disease if one is
inserted into a gene (e.g., hemophilia A).
• LINEs-2 and -3 are inactive because reverse
transcription from the 3’ end often fails to
proceed to the 5’ end
33.
34. Short interspersed nuclear elements (SINEs)
• SINEs are found in a diverse array of
eukaryotic species, including mammals,
amphibians, and sea urchins.
• Each species with SINEs has its own
characteristic array of SINE families.
• A well-studied SINE family is the Alu family of
certain primates.
35. • This family is named for the cleavage site for the
restriction enzyme AluI typically found in the
repeated sequence.
• In humans, the Alu family is the most abundant SINE
family in the genome, consisting of 200–300-bp
sequences repeated as many as a million times and
making up about 10% of the human genome.
• One Alu repeat is located every 5,000 bp in the
genome, on average.
36. • The SINEs are also transposons, but they do
not encode the enzymes they need for
movement. They can move, however, if those
enzymes are supplied by an active LINE
transposon.
• SINEs can be best described as
nonautonomous LINEs, because they have the
structural features of LINEs but do not encode
their own reverse transcriptase
37.
38. Role of LINEs and SINEs
• While historically viewed as "junk DNA",
recent research suggests that in some rare
cases both LINEs and SINEs were incorporated
into novel genes, so as to evolve new
functionality.
• The distribution of these elements has been
implicated in some genetic diseases and
cancers.
39.
40. Tandem Repeats
• However, some moderately and highly
repetitive sequences are clustered together in
a tandem array, also known as tandem
repeats.
• In a tandem array, a very short nucleotide
sequence is repeated many times in a row.
• In Drosophila, for example, 19% of the
chromosomal DNA is highly repetitive DNA
found in tandem arrays.
41. • Depending on the average size of the arrays of
repeat units, highly repetitive noncoding DNA
belonging to this class can be grouped into
three subclasses: satellite, minisatellite and
microsatellite DNA.
– Classical satellite DNA: repeat unit 100-5000 kb
– Minisatellite DNA: 100 bp – 20 kb
– Microsatellite DNA: <150bp; usually 4 bp or less
42.
43. Satellite DNA
• Human satellite DNA is comprised of very
large arrays of tandemly repeated DNA with
the repeat unit being a simple or moderately
complex sequence (100kb to several Mb)
• Repeated DNA of this type is not transcribed
• Accounts for the bulk of the heterochromatic
regions of the genome, being notably found in
the vicinity of the centromeres.
44.
45.
46. Minisatellite DNA
• Minisatellite DNA comprises a collection of
moderately sized arrays of tandemly repeated
DNA sequences which are dispersed over
considerable portions of the nuclear genome
• Like satellite DNA sequences, they are not
normally transcribed
• Arrays often within 0.1-20kb range
47. Minisatellite DNA
• In humans, 90% of minisatellites are found at the
sub-telomeric region of chromosomes.
• The telomere sequence itself is a tandem repeat:
TTAGGG TTAGGG TTAGGG .
• Variation in size (array length) of these regions
between individuals in humans was originally the
basis for DNA fingerprinting.
48. Minisatellite DNA
• Hypervariable minisatellite DNA
– many of the arrays are found near the telomeres
– 9-64bp repeating unit with array of 0.1–20 kb
long.
• Telomeric DNA
– 10–15 kb of tandem hexanucleotide repeat units,
especially TTAGGG, which are added by a
specialized enzyme, telomerase
49. Microsatellites (SSRs, STRs)
• Also known as Short Tandem Repeat (STR), Simple
Sequence length polymorphism (SSLP) and
Simple Sequence Repeat (SSR)
• Repeating sequences of 1-6 base pairs of DNA and
can be repeated 10 to 100 times.
• Most common in humans is the (CA)n sequence
where n varies from 5 -50 or more.
• Found on average every 10kbp in the human genome
51. • Trinucleotide and tetranucleotide tandem repeats
are comparatively rare.
• The lengths of particular microsatellite sequences
tend to be highly variable among individuals. These
differences make up molecular "alleles".
• Although microsatellite DNA has generally been
identified in intergenic DNA or within the introns of
genes, a few examples have been recorded within
the coding sequences of genes.
52. VNTR
• At a tandem repeat site, the number of repeats
varies widely in the population, although the repeat
number is usually well preserved during
transmission.
• Therefore each different repeat number can be
treated as a separate "allele" and the site can be
treated as a highly polymorphic site with multiple
alleles. Such a site is known as a VNTR (variable
number of tandem repeats) site.
53. VNTR
• A Variable Number Tandem Repeat (or VNTR) is a location in
a genome where a short nucleotide sequence is organized as
a tandem repeat.
• These can be found on many chromosomes, and often show
variations in length between individuals.
54. VNTR
• Each variant acts as an inherited allele,
allowing them to be used for personal or
parental identification. Their analysis is useful
in genetics and biology research, forensics,
and DNA fingerprinting, DNA profiling.
• Two principal families of VNTRs:
microsatellites and minisatellites
55. VNTR
• VNTR via recombination or replication errors,
leading to alleles with different numbers of
repeats
56.
57. VNTR
• A Variable Number Tandem Repeat (or VNTR) is a location in
a genome where a short nucleotide sequence is organized as
a tandem repeat.
• These can be found on many chromosomes, and often show
variations in length between individuals.