Minisatellites are sections of DNA that contain short repeating sequences between 10-60 base pairs in length. They occur at over 1,000 locations in the human genome. Minisatellites are distinguished from microsatellites by the size of the repeating sequences, with microsatellites containing repeats of 1-7 base pairs and minisatellites containing repeats of 10-100 base pairs or more. Minisatellites contain repetitive GC-rich sequences that vary in length and are found in tandem arrays, making them useful for studying DNA mutation mechanisms. Due to their high level of polymorphism, minisatellites have been extensively used for DNA fingerprinting and genetic analysis.
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.
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
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.
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.
SNP (Single Nucleotide Polymorphic), SNP mapping, SNP profile, SNP types, SNP analysis by gel electropherosis and by mass spectrometry, SNP effects, single strand conformation polymorphism, SNP advantages and disadvantages and application of SNP profile in drug choice
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.
Techniques based on the principle of selectively amplifying a subset of restriction fragments from a complex mixture of DNA fragments obtained after digestion of genomic DNA with restriction endonucleases.
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
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
Techniques based on the principle of selectively amplifying a subset of restriction fragments from a complex mixture of DNA fragments obtained after digestion of genomic DNA with restriction endonucleases.
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
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
In your own words, define the following terms. Concentrate on structu.pdfaromanets
In your own words, define the following terms. Concentrate on structural make-up, location, and
inter-relationships, if any. variable-number tandem repeats (VNTRs) microsatellite DNA
minisatellite DNA long interspersed elements (LINEs) short interspersed elements (SINEs)
telomeric repeats centromeric satellite DNA
Solution
Answer :
a. ) VNTR\'S : The short strectch of nucleotide sequence is organized as a tandem repeat in the
genome which are variable in number of tandem repeat (or VNTR) . These can be found on
many chromosomes, and often show variations in length between individuals. These play a very
important role in DNA fingerprinting, studying the population.
b) Microsatellite DNA : These are di-, tri-, or tetra nucleotide tandem repeats in DNA sequences.
where in the number of repeats is variable in populations of DNA and within the alleles of an
individual. The sequence has a 20 dinucleotide repeat (40bp) stretch. These are developed by
sequencing the exon portion of the gene which varies between individual to individual. These
help in construction of geneitic linkage maps, function of various genes , study of genes by
knocking out the function. These are co dominantly inherited in mendialian seggregation.
c): Minisatellite DNA : A minisatellite is a tract of repetitive DNA in which certain DNA motifs
(ranging in length from 10–60 base pairs) are typically repeated 5-50 times. Minisatellites occur
at more than 1,000 locations in the human genome and they are notable for their high mutation
rate and high diversity in the population.They are generally GC rich and variant repats are
tandemly intermingled, which make the minisatellites ideal for studying DNA turnover
mechanisms. They are also called variable number of Tandem repats because the number of
repats in a given mini satellite vaies gratly among individuals.
d) LINES : These are Long interspersed nucleotide sequences these are active or degenerate
descendants of transposable elements. these are related to LTR transposons, but distinct in their
structure
e) SINES : These are nothing but Short interspersed Nucleotide sequences, these are Non-
autonomous transposable elements (lacking the ability to mediate their own transposition) and
their degenerate descendents. these are originally derived from tRNA sequences and distinct
from retrotransposons
SINEs are retrosequences that range in length from 75 to 500 bp, do not possess any reading
frame,Thus their retroposition mustbe aided by other genetic elements . These elements lack
LTR\'s and introns, possess an encoded poly A tail .SINEs require cross mobilisation for
transposition.
f)Telomere repeats : A telomere is a region of repititive nucleotide sequences at each end of the
chromosome, which protect the end of the chromosome from deteriotation or from fusion with
neighbouring chromosomes this sequence of TTAGGG is frequently repeated approximately
2500 times in humans. Telomeric repats are the tandem arrays of a short G rich sequen.
Nuclear Genomes(Short Answers and questions)Zohaib HUSSAIN
1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising?
Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive.
2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared?
Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA.
3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high?
Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated.
4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods?
Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown.
5. What is the function of the different genes in the human globin gene families?
Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
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Welcome to UiPath Test Automation using UiPath Test Suite series part 5. In this session, we will cover CI/CD with devops.
Topics covered:
CI/CD with in UiPath
End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
Pushing the limits of ePRTC: 100ns holdover for 100 daysAdtran
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• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
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Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
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My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
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My slides at Nordic Testing Days 6.6.2024
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Alt. GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using ...James Anderson
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The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
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Bob Boule
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Gopinath Rebala
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1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
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Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
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https://arxiv.org/abs/2306.08302
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PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
2. minisatellite (also referred as VNTR) is a section
of DNA that consists of a short series of bases
10–60 bp.[1][2] These occur at more than 1,000
locations in the human genome.
Minisatellites have been confused with
Microsatellites (also called as Short Tandem
Repeats or STRs). STRs are also repeated
sequences, but they are usually 2–13 nucleotides
long. The term minisatellite has been
interchangeably used with variable number
tandem repeats (VNTRs).
3. They are usually distinguished according to the
size of the repeats:
Microsatellites, also termed Short tandem repeats
(STRs) consist of tracts of repeats of 1-7bp, and
minisatellites also called (VNTR) usually contain
repeats of longer length (100-several hundred bp)
Minisatellites can be found in tandem arrays, but
the majority are interspersed in the genome.
Whilst microsatellites are found mostly in tandem
repeats.
4. Minisatellites" consist of repetitive, generally GC-rich, variant repeats
that range in length from 10 to over 100 bp. These variant repeats are
tandemly intermingled, which makes minisatellites ideal for studying
DNA turnover mechanisms.
Some minisatellites contain a central (or "core") sequence of letters
“GGGCAGGANG” (where N can be any base) or more generally a
strand bias with purines (adenosine (A) and guanine (G)) on one strand
and pyrimidines (cytosine (C) and thymine (T)) on the other. It has been
proposed that this sequence encourages chromosomes to swap DNA.
In alternative models, it is the presence of a neighbouring cis-acting
meiotic double-strand break hotspot which is the primary cause of
minisatellite repeat copy number variations. Somatic changes are
suggested to result from replication difficulties (which might include
replication slippage, among other phenomena). When such events
occur, mistakes are made, thus causing minisatellites at over 1,000
locations in a person's genome to have slightly different numbers of
repeats, thereby making each individual unique. The most highly
mutable minisatellite locus described so far is CEB1 (D2S90) described
by Vergnaud
5. Since the fortuitous discovery of the first human
minisatellite in 1980 by A.R. Wyman and R. White[4]
and especially the discovery that the extreme
polymorphism of minisatellites made them superb for
DNA fingerprinting by Alec Jeffreys,[5] this class of
repeats has been an intense focus of studies that
have addressed the turnover mechanisms that
provoke their instability. Due to their high level of
polymorphism, minisatellites have been extensively
used for DNA fingerprinting as well as for genetic
markers in linkage analysis and population studies.
Minisatellites have also been implicated as regulators
of gene expression (e.g., at levels of
transcription, alternative splicing, or imprint control) or
6. Multi locus probes Repetitive DNA. A major step forward in genetic identification is the
discovery that about 30–90% of the genome of virtually all the species is constituted by
regions of repetitive DNA, which are highly polymorphic in nature. These regions contain
genetic loci comprising several hundred alleles, differing from each other with respect to
length, sequence or both and they are interspersed in tandem arrays ubiquitously. The
repetitive DNA regions play an important role in absorbing mutations in the genome. Of the
mutations that occur in the genome, only inherited mutations play a vital role in evolution or
polymorphism. Thus repetitive DNA and mutational forces functional in nature together form
the basis of a number of marker systems that are useful for various applications in plant
genome analysis. The markers belonging to this class are both hybridization-based and
PCR-based.
Microsatellites and minisatellites. The term microsatellites was coined by Litt and
Lutty26, while the term minisatellites was introduced by Jeffrey2. Both are multilocus probes
creating complex banding patterns and are usually non-species specific occurring
ubiquitously. They essentially belong to the repetitive DNA family. Fingerprints generated by
these probes are also known as oligonucleotide fingerprints. The methodology has been
derived from RFLP and specific fragments are visualized by hybridization with a labelled
micro- or minisatellite probe.
Minisatellites are tandem repeats with a monomer repeat length of about 11–60 bp, while
microsatellites or short tandem repeats/simple sequence repeats (STRs/
SSRs) consist of 1 to 6 bp long monomer sequence that is repeated several times. These
loci contain tandem repeats that vary in the number of repeat units between genotypes and
are referred to as variable number of tandem repeats (VNTRs) (i.e. a single locus that
contains variable number of tandem repeats between individuals27) or hypervariable regions
(HVRs) (i.e. numerous loci containing tandem repeats within a genome generating high
levels of polymorphism between individuals2). Microsatellites and minisatellites thus form an
ideal marker system creating complex banding patterns by simultaneously detecting multiple
DNA loci. Some of the prominent features of these markers are that they are dominant
fingerprinting markers and codominant STMS (sequence tagged microsatellites) markers.
Many alleles exist in a population, the level of heterozygosity is high and they follow
7. Minisatellite and microsatellite sequences converted into PCR-based markers Sequence-tagged microsatellite site markers
(STMS). This method includes DNA polymorphism using specific primers designed from the sequence data of a specific locus.
Primers complementary to the flanking regions of the simple sequence repeat loci28 yield highly polymorphic amplification
products. Polymorphisms appear because of variation in the number of tandem repeats (VNTR loci) in a given repeat motif. Tri-
and tetranucleotide microsatellites are more popular for STMS analysis because they present a clear banding pattern after PCR
and gel electrophoresis29. However, dinucleotides are generally abundant in genomes and have been used as markers e.g.
(CA)n(AG)n and (AT)n (ref. 30). The di- and tetranucleotide repeats are present mostly in the non-coding regions of the
genome, while 57% of trinucleotide repeats are shown to reside in or around the genes. A very good relationship between the
number of alleles detected and the total number of simple repeats within the targeted microsatellite DNA has been observed. Thus
larger the repeat number in the microsatellite DNA, greater is the number of alleles detected in a large population31.
Direct amplification of minisatellite DNA markers (DAMD-PCR). This technique, introduced by Heath et al.32, has been explored as
a means of generating DNA probes useful for detecting polymorphism. DAMD-PCR clones can yield individual-specific DNA
fingerprinting pattern and thus have the potential as markers for species differentiation and cultivar identification33.
Inter simple sequence repeat markers (ISSR). In this technique, reported by Zietkiewicz et al.34, primers based on microsatellites
are utilized to amplify inter-SSR DNA sequences. Here, various microsatellites anchored at the 3¢ end are used for amplifying
genomic DNA which increases their specificity. These are mostly dominant markers, though occasionally a few of them exhibit
codominance. An unlimited number of primers can be synthesized for various combinations of di-, tri-, tetra- and pentanucleotides
[(4)3 = 64, (4)4 = 256] etc. with an anchor made up of a few bases and can be exploited for a broad range of applications in plant
species. Other repetitive DNA-type markers Transposable elements. A large number of transposable repeat elements have been
studied in plants; however, only a few have been exploited as molecular markers. In evolutionary terms, they have contributed to
genetic differences between species and individuals by playing a role in retrotransposition events promoting unequal crossing over.
Retrotransposon-mediated fingerprinting has been shown to be an efficient fingerprinting method for detection of genetic
differences between different species.
Alu-repeats. This strategy was developed to fingerprint genotypes using semispecific primers, complementary to repetitive DNA
elements called ‘Alu-repeats’, in human genome analysis. Alu repeats are a class of randomly repeated interspersed
DNA, preferentially used for Alu PCR as they reveal considerable levels of polymorphism35. These representatives of short and
long interspersed nuclear elements are known as SINES. Alu elements are approximately 300 bp in size and have been suggested
to be originated from special RNA species that have been reintegrated at a rate of approximately one integration event per 10000
years. These repeats have been studied largely in humans, while their function in plants remains largely unexplored.
Repeat complementary primers. As an alternative to the interspersed repeats, primers complementary to other repetitive sequence
elements were also successfully used for generation of polymorphisms, e.g. introns/exons splice junctions36, tRNA
genes37, 5sRNA genes38 and Zn-finger protein genes39. Primers complementary to specific exons, resulting in the amplification of
the intervening introns have been studied by Lessa et al.40
. One of the strengths of these new strategies is that they are more
amenable to automation than the conventional hybridization-based techniques