DNA sequencing is a laboratory technique used to determine the exact sequence of bases (A, C, G, and T) in a DNA molecule. The DNA base sequence carries the information a cell needs to assemble protein and RNA molecules. DNA sequence information is important to scientists investigating the functions of genes.
In medicine, DNA sequencing is used for a range of purposes, including diagnosis and treatment of diseases. In general, sequencing allows health care practitioners to determine if a gene or the region that regulates a gene contains changes, called variants or mutations, that are linked to a disorder.
The chain-termination method developed by Frederick Sanger and coworkers in 1977. This method used fewer toxic chemicals and lower amounts of radioactivity than the Maxam and Gilbert method. Because of its comparative ease, the Sanger method was soon automated and was the method used in the first generation of DNA sequencers.
The chain-termination method developed by Frederick Sanger and coworkers in 1977. This method used fewer toxic chemicals and lower amounts of radioactivity than the Maxam and Gilbert method. Because of its comparative ease, the Sanger method was soon automated and was the method used in the first generation of DNA sequencers.
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.
To modifying the structure of a specific gene.
Gene targeting vector introduced into the cell.
Vector modifies the normal chromosomal gene through homologous recombination.
Useful in treating some human genetic disorders – Hemophilia, Duchenne Muscular Dystrophy.
Treating human diseases by genetic approaches – Gene Therapy.
Gene Therapy – Replacing the defective gene by normal copy of the gene.
Expressed sequence tag/EST is a short partial sequence, typically 200-400 bp long, of a complimentary DNA/Cdna.
EST is a short sub-sequence of a cDNA sequence.
Used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.
Approximately 74.2 million ESTs are available in public databases.
EST results from one-short sequencing of a cloned cDNA.
Low-quality fragments.
Length is approximately 500 to 800 nucleotides.
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.
DNA Sequencing : Maxam Gilbert and Sanger SequencingVeerendra Nagoria
DNA sequencing is a technique to find out the exact arrangement of Nucleotides to make one strand of DNA. DNA sequencing helps in numerous ways from sequence information to paternity testing, mutation detection etc. Traditionally two approaches were used to solve the problem. First is based of enzymes and Second is based on ddNTPs to sequence the DNA using gel electrophoresis technique.
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.
Techniques of DNA Extraction, Purification and QuantificationBHUMI GAMETI
Introduction
The overall process…
Uses of isolated genomic DNA
Extraction of DNA from plant material
Components of DNA extraction solutions
Cell Lysis or Cell disruption :
Purification of DNA
CTAB Method
Phenol–chloroform extraction
PROTEINASE K
Salting out
Silica adsorption method
Magnetic beads
FTA Paper
Nucleic acid quantification
Agarose Gel Electrophoresis
UV spectroscopy
DNA quantification using NanoDrop
Synopsis
Introduction
Some Facts
Types of SNPs
SNPs act as gene markers
Methods of Detection
Techniques to detect SNPs
Allelic Specific Cleavage
Differential Hybridization
Single Base Extension or minisequencing
Alternate Methods for Detecting SNPs
Mass Spectrometry
Microchips
SIGNIFICANCE OF SNPs
HAPLOTYPE
ADVANTAGES
Are SNP data available to the public?
Some important SNP database Resources
CONCLUSION
References
Use of DNA barcoding and its role in the plant species/varietal Identifica...Senthil Natesan
Plant DNA barcoding research is shifting beyond performance comparisons of different DNA regions towards practical applications. The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1(CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. The studies on cucumis sp for the application of DNA barcode shows the possibility of discrimination at species level not the varietal level using the matK gene barcode. The phylogenetic tree constructed by using matK gene sequences clearly differentiated the species C. sativus and C. melo which will help for the future application in cucumis taxonomy and phylogeny studies
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.
To modifying the structure of a specific gene.
Gene targeting vector introduced into the cell.
Vector modifies the normal chromosomal gene through homologous recombination.
Useful in treating some human genetic disorders – Hemophilia, Duchenne Muscular Dystrophy.
Treating human diseases by genetic approaches – Gene Therapy.
Gene Therapy – Replacing the defective gene by normal copy of the gene.
Expressed sequence tag/EST is a short partial sequence, typically 200-400 bp long, of a complimentary DNA/Cdna.
EST is a short sub-sequence of a cDNA sequence.
Used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.
Approximately 74.2 million ESTs are available in public databases.
EST results from one-short sequencing of a cloned cDNA.
Low-quality fragments.
Length is approximately 500 to 800 nucleotides.
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.
DNA Sequencing : Maxam Gilbert and Sanger SequencingVeerendra Nagoria
DNA sequencing is a technique to find out the exact arrangement of Nucleotides to make one strand of DNA. DNA sequencing helps in numerous ways from sequence information to paternity testing, mutation detection etc. Traditionally two approaches were used to solve the problem. First is based of enzymes and Second is based on ddNTPs to sequence the DNA using gel electrophoresis technique.
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.
Techniques of DNA Extraction, Purification and QuantificationBHUMI GAMETI
Introduction
The overall process…
Uses of isolated genomic DNA
Extraction of DNA from plant material
Components of DNA extraction solutions
Cell Lysis or Cell disruption :
Purification of DNA
CTAB Method
Phenol–chloroform extraction
PROTEINASE K
Salting out
Silica adsorption method
Magnetic beads
FTA Paper
Nucleic acid quantification
Agarose Gel Electrophoresis
UV spectroscopy
DNA quantification using NanoDrop
Synopsis
Introduction
Some Facts
Types of SNPs
SNPs act as gene markers
Methods of Detection
Techniques to detect SNPs
Allelic Specific Cleavage
Differential Hybridization
Single Base Extension or minisequencing
Alternate Methods for Detecting SNPs
Mass Spectrometry
Microchips
SIGNIFICANCE OF SNPs
HAPLOTYPE
ADVANTAGES
Are SNP data available to the public?
Some important SNP database Resources
CONCLUSION
References
Use of DNA barcoding and its role in the plant species/varietal Identifica...Senthil Natesan
Plant DNA barcoding research is shifting beyond performance comparisons of different DNA regions towards practical applications. The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1(CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. The studies on cucumis sp for the application of DNA barcode shows the possibility of discrimination at species level not the varietal level using the matK gene barcode. The phylogenetic tree constructed by using matK gene sequences clearly differentiated the species C. sativus and C. melo which will help for the future application in cucumis taxonomy and phylogeny studies
Describe the steps in Sanger DNA sequencing. Provide a high level des.pdffatoryoutlets
Consider the program: var s: int:= 1, i: int co i:= 1 to 2 rightarrow do true rightarrow (await s >
0 rightarrow s: = s - 1) (s:= s + 1) Above, S_i is a statement list that is assumed not to modify
shared variable s. Develop complete proof outlines for the two processes. Demonstrate that the
proofs of the processes are interference-free. Then use the proof outlines and the method of
Exclusion of Configurations (2.25) to show that S_1 and S_2 cannot execute at the same time
and that the program is deadlock-free. What scheduling policy is required to ensure that a
process delayed at its first await statement will eventually be able to proceed? Explain.
Solution
int i=1
do(i=1 to 2)
{
wait(s>0){
s=s-1
Si
}
s=s+1
}
to prove that it should be deadlock free it should support mutual exclusion,progress,bounded
waiting.
mutual exclusion:-
p1:
int i=1
do(i=1 to 2) //entry section
{
wait(s>0){ //critical section
s=s-1
Si
}
s=s+1
} //exit section
so while p1 is exexcuting p2 while s enters into critical section as we don\'t update any values so
mutual exclusion is possible and can be formed.
progress:-
when p1 is in non-critical section p2can execute in critical section.program gurantees progress.
bounded-waiting :-
suitable for ony countable no of procedures and processes.
as it satisfies all properties ....so it\'s deadlock free..
DNA Sequencing - DNA sequencing is like reading the instructions inside a cellAmitSamadhiya1
DNA sequencing is like reading the instructions inside a cell. It's figuring out the exact order of the building blocks that make up our DNA, represented by the letters A, T, C, and G. This order is like a code that tells our bodies how to function and grow.
By reading this code, scientists can understand genes, diagnose diseases, and even trace our ancestry. There are different ways to sequence DNA, kind of like having a few different ways to read a book. These techniques are constantly improving, making it faster and easier to unlock the secrets hidden in our DNA.
Describe in your own words the benefits, but also the problems of ha.pdfarenamobiles123
Describe in your own words the benefits, but also the problems of having the human genome
deciphered. Write several paragraphs.
Solution
The history of the human race has been filled with curiosity and discovery about our abilities and
limitations. As an egotistical creature with a seemingly unstoppable desire for new
accomplishments, we attempt feats with emotion and tenacity. People worldwide raced to be the
first to discover the secrets and the ability of flight. Enormous amounts of monies were spent on
sending people into space and the race to land on the moon. With the rapid growth of scientific
knowledge and experimental methods, humans have begun to unravel and challenge another
mystery, the discovery of the entire genetic make-up of the human body.
This endeavor, the Human Genome Project (HGP), has created hopes and expectations about
better health care. It has also brought forth serious social issues. To understand the potential
positive and negative issues, we must first understand the history and technical aspects of the
HGP.
History of the Human Genome Project
The HGP has an ultimate goal of identifying and locating the positions of all genes in the human
body. A researcher named Renato Dulbecco first suggested the idea of such a project while the
U.S. Department of Energy (DOE) was also considering the same project because issues related
to radiation and chemical exposure were being raised. Military and civilian populations were
being exposed to radiation and possible carcinogenic chemicals through atomic testing, the use
of Agent Orange in Vietnam, and possible nuclear power facility accidents. Genetic knowledge
was needed to determine the resiliency of the human genome.
Worldwide discussion about a HGP began in 1985. In 1986, the DOE announced its\' Human
Genome Initiative which emphasized the development of resources and technologies for genome
mapping, sequencing, computation, and infrastructure support that would lead to the entire
human genome map. United States involvement began in October 1990 and was coordinated by
the DOE and the National Institute of Health (NIH). With an estimated cost of 3 billion dollars,
sources of funding also include the National Science Foundation (NSF) and the Howard Hughes
Medical Institute (HHMI). Because of the involvement of the NIH, DOE, and NSF who receive
U.S. Congressional funding, the HGP is partly funded through federal tax dollars. Expected to
last 15 years, technological advancements have accelerated the expected date of completion to
the year 2003. This completion date would coincide with the 50th anniversary of Watson and
Crick\'s description of the structure of DNA molecule.
Human Genome Project Goals
The specific goals of the HGP are to::
Technical Aspects of the HGP
Mapping Strategies
To sequence the human genome, maps are needed. Physical maps are a series of overlapping
pieces of DNA isolated in bacteria. Physical maps are used to describe the DNA\'s chemical
characteristics..
Biotechnology is technology that utilizes biological systems, living organisms or parts of this to develop or create different products. Brewing and baking bread are examples of processes that fall within the concept of biotechnology (use of yeast (= living organism) to produce the desired product).
DNA consists of a linear string of nucleotides, or bases, for simplicity, referred to by the first letters of their chemical names--A, T, C and G. The process of deducing the order of nucleotides in DNA is called DNA sequencing. Since the DNA sequence confers information that the cell uses to make RNA molecules and proteins, establishing the sequence of DNA is key for understanding how genomes work. The technology for DNA sequencing was made faster and less expensive as a part of the Human Genome Project. And recent developments have profoundly increased the efficiency of DNA sequencing even further.
DNA sequencing refers to the general laboratory technique for determining the exact sequence of nucleotides, or bases, in a DNA molecule. The sequence of the bases (often referred to by the first letters of their chemical names: A, T, C, and G) encodes the biological information that cells use to develop and operate. Establishing the sequence of DNA is key to understanding the function of genes and other parts of the genome. There are now several different methods available for DNA sequencing, each with its own characteristics, and the development of additional methods represents an active area of genomics research.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
The three important techniques of biotechnology are: (1) Recombinant DNA Technology (Genetic Engineering) (2) Plant Tissue Culture and (3) Transgenic (Genetically Modified Organisms).
Western blotting is a laboratory technique used to detect a specific protein in a blood or tissue sample. The method involves using gel electrophoresis to separate the sample's proteins. The separated proteins are transferred out of the gel to the surface of a membrane.
Southern, northern, and western blot protocols are similar, and begin with electrophoretic separation of protein and nucleic acid fragments on a gel, which are then transferred to a membrane (nitrocellulose membrane, polyvinylidene difluoride (PVDF) membrane, etc.) where they are immobilized.
Southern blotting is a hybridization technique for identification of particular size of DNA from the mixture of other similar molecules. This technique is based on the principle of separation of DNA fragments by gel electrophoresis and identified by labelled probe hybridization.
Animal Tissue Culture
The foundation of animal cell and tissue culture was laid by Jolly (1903) when he showed that animal cells could not only survive but could divide in culture medium. The actual beginning of animal cell culture and tissue culture was made by Harrison (1907) and later by Carrel (1912) who used frog’s tissue in tissue culture. They successfully showed that animal cells can be grown indefinitely in culture medium just like microorganisms. Later tissues from warm blooded animals like chick and mammals were used as material for tissue culture purpose.
There are three methods commonly used to initiate a culture from animals.
Organ culture. Whole organs from embryos or partial adult organs are used to initiate organ culture in vitro. ...
Primary explant culture. Fragments exercised from animal tissue may be maintained in a number of different ways. ...
Cell culture.
Biotechnology and its applications
The applications of biotechnology include therapeutics, diagnostics, genetically modified crops for agriculture, processed food, bioremediation, waste treatment, and energy production.
Assisted reproductive technology treats infertility and the treatment involves both a man's sperm and a woman's egg. The procedure begins by extracting eggs from a woman's body and then fusing it with the sperm to generate embryos. This embryo is then transferred back into the woman's body.
Southern Blot is the analytical technique used in molecular biology, immunogenetics and other molecular methods to detect or identify DNA of interest from a mixture of DNA sample or a specific base sequence within a strand of DNA. The technique was developed by a molecular biologist E.M. Southern
Principle of DNA Microarray Technique
The principle of DNA microarrays lies on the hybridization between the nucleic acid strands.
The property of complementary nucleic acid sequences is to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.
DNA fingerprinting is a technique used to identify and analyze the variations in various individuals at the level of DNA. DNA fingerprinting involves identifying differences in some specific regions in DNA sequence called as repetitive DNA because, in these sequences, a small stretch of DNA is repeated many times.
Biotechnology is defined as the broad area of biology which uses both the technology and the application of living organisms and their components to develop, modify and produce useful products for human welfare. The term ‘Biotechnology’ was coined in the year 1919 by an agricultural engineer Karoly Ereky, hence he is called as the father of Biotechnology.
Principles of Biotechnology
According to modern Biotechnology, the main principles of Biotechnology are:
Genetic engineering, which is used to modify the DNA of the target organism, thereby changing the phenotype of the organism.
Bioprocess engineering, which is the maintenance of sterile conditions to support the growth of large quantities of desired microbes and other eukaryotic cells which are used for the production of new or modified biotechnological products such as antibiotics, enzymes, vaccines, etc.
The techniques of genetic engineering mainly include:
DNA fragment is isolated from the donor organism.
It is inserted into the vector DNA.
It is transferred into an appropriate host.
Cloning of the recombinant DNA in the host organism.
The DNA microarray is a tool used to determine whether the DNA from a particular individual contains a mutation in genes like BRCA1 and BRCA2. The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes.
This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000’s of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
Boyd 2014 [16] Record linkage is the process of bringing together data relating to the same individual from within and between different datasets. When a unique person-based identifier exists, linkage can be achieved by simply merging datasets on the identifier.
Linkage is the close association of genes or other DNA sequences on the same chromosome. The closer two genes are to each other on the chromosome, the greater the probability that they will be inherited together.
The two different types of linkage are:
Complete linkage.
Incomplete linkage.
“Linkage and recombination are the phenomena that describe the inheritance of genes.”
Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears.
An example of epistasis is the interaction between hair colour and baldness. A gene for total baldness would be epistatic to one for blond hair or red hair. The hair-colour genes are hypostatic to the baldness gene. The baldness phenotype supersedes genes for hair colour, and so the effects are non-additive.
Various types of epistatic gene interaction are 1) Recessive epitasis (9:3:4) 2) Dominant epistasis (12:3:1) 3) Dominant and recessive (inhibitory) epistasis (13:3) 4) Duplicate recessive epistasis (9:7) 5) Duplicate dominant epistasis (15:1) and 6) Polymeric gene interaction (9:6:1).
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
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
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
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.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
2024.06.01 Introducing a competency framework for languag learning materials ...
-DNA Sequencing Notes.pdf
1. B.Sc.III, Sem-VI (ZOOLOGY)
NOTES ON DNA SEQUENCING
Authored By: Dr. Rajendra Chavhan, RMG College Nagbhid
DNA Sequencing Definition
DNA sequencing is the process of determining the sequence of nucleotides within a
DNA molecule. Every organism’s DNA consists of a unique sequence of nucleotides.
Determining the sequence can help scientists compare DNA between organisms, which can
help show how the organisms are related.
DNA Sequencing Overview
This means that by sequencing a stretch of DNA, it will be possible to know the order
in which the four nucleotide bases – adenine, guanine, cytosine, and thymine – occur within
that nucleic acid molecule.
The necessity of DNA sequencing was first made obvious by Francis Crick’s theory
that the sequence of nucleotides within a DNA molecule directly influenced the amino acid
sequences of proteins. At the time, the belief was that a completely sequenced genome would
lead to a quantum leap in understanding the biochemistry of cells and organisms.
Modern DNA sequencing consists of high-throughput methods which allow entire
DNA sequences to be discovered in a matter of hours. This technology has allowed many
companies to start offering at-home DNA testing. Many of the “results” found by these tests
are simply correlations found between a genetic variant and a certain condition. However,
technology has also allowed scientists to test the DNA of many organisms to better understand
evolutionary relationships.
DNA Sequencing Example
Though DNA sequencing used to take years, it can now be done in hours. Further, the
first full sequence of human DNA took around 3 billion dollars. Now, certain companies
will sequence your entire genome for less than $1,000. The most advanced tests will analyze
every nucleotide within your genome. However, many companies now offer single-nucleotide
polymorphism tests.
These tests focus on individual nucleotides within genes that can signify certain genetic
variants. These SNPs, as they are known, have been correlated to certain conditions and
can help predict how your genes may influence your life. Some SNPs are related to various
diseases, while others are related to your metabolism and how your body processes nutrients.
Thousands of different correlations have been found, and DNA sequencing can be used to
figure out how your genome affects your life.
DNA Sequencing Methods
There are two main types of DNA sequencing. The older, classical chain termination
method is also called the Sanger method. Newer methods that can process a large number of
DNA molecules quickly are collectively called High-Throughput Sequencing (HTS)
techniques or Next-Generation Sequencing (NGS) methods.
Sanger Sequencing
2. The Sanger method relies on a primer that binds to a denatured DNA molecule and
initiates the synthesis of a single-stranded polynucleotide in the presence of a DNA
polymerase enzyme, using the denatured DNA as a template. In most circumstances, the
enzyme catalyzes the addition of a nucleotide. A covalent bond, therefore, forms between the
3′ carbon atom of the deoxyribose sugar molecule in one nucleotide and the 5′ carbon atom of
the next. This image below shows how this bond is formed.
A sequencing reaction mixture, however, would have a small proportion of modified
nucleotides that cannot form this covalent bond due to the absence of a reactive hydroxyl group,
giving rise to the term ‘dideoxyribonucleotides’, i.e., they do not have a 2’ or 3’ oxygen atom
when compared to the corresponding ribonucleotide. This would terminate the DNA
polymerization reaction prematurely. At the end of multiple rounds of such
polymerizations, a mixture of molecules of varying lengths would be created.
In the earliest attempts at using the Sanger method, the DNA molecule was first
amplified using a labeled primer and then split into four test tubes, each having only one type
of ddNTP. That is, each reaction mixture would have only one type of modified nucleotide that
could cause chain termination. After the four reactions were completed, the mixture of DNA
molecules created by chain termination would undergo electrophoresis on a polyacrylamide
gel, and get separated according to their length.
3. In the image above, a sequencing reaction with ddATP was electrophoresed through
the first column. Each line represents a DNA molecule of a particular length, the result of a
polymerization reaction that was terminated by the addition of a ddATP nucleotide. The
second, third and fourth columns contained ddTTP, ddGTP, and ddCTP respectively.
With time, this method was modified so that each ddNTP had a different
fluorescent label. The primer was no longer the source of the radiolabel or fluorescent tag.
Also known as dye-terminator sequencing, this method used four dyes with non-overlapping
emission spectra, one for each ddNTP.
The image shows the difference between labeled primers,
labelled dNTPs and dyed terminator NTPs.
4. The image above shows a schematic representation of dye-terminator sequencing.
There is a single reaction mixture carrying all the elements needed for DNA elongation. The
reaction mixture also contains small concentrations of four ddNTPs, each with a different
fluorescent tag. The completed reaction is run on a capillary gel. The results are obtained
through an analysis of the emission spectra from each DNA band on the gel. A software
program then analyzes the spectra and presents the sequence of the DNA molecule.
High Throughput Sequencing
Sanger sequencing continues to be useful for determining the sequences of relatively
long stretches of DNA, especially at low volumes. However, it can become expensive and
laborious when a large number of molecules need to be sequenced quickly. Ironically,
though the traditional dye-terminator method is useful when the DNA molecule is longer, high-
throughput methods have become more widely used, especially when entire genomes need to
be sequenced.
There are three major changes compared to the Sanger method. The first was the
development of a cell-free system for cloning DNA fragments. Traditionally, the stretch of
DNA that needed to be sequenced was first cloned into a prokaryotic plasmid and amplified
within bacteria before being extracted and purified. High throughput sequencing or next-
generation sequencing technologies no longer relied on this labor-intensive and time-intensive
procedure.
Secondly, these methods created space to run millions of sequencing reactions in
parallel. This was a huge step forward from the initial methods where eight different
reaction mixtures were needed to produce a single reliable nucleotide sequence. Finally,
there is no separation between the elongation and detection steps. The bases are identified as
the sequencing reaction proceeds. While HTS decreased cost and time, their ‘reads’ were
relatively short. That is, in order to assemble an entire genome, intense computation is
necessary.
The advent of HTS has vastly expanded the applications for genomics. DNA
sequencing has now become an integral part of basic science, translational research, medical
diagnostics, and forensics.
Uses of DNA Sequencing
5. Traditional, chain-termination technology and HTS methods are used for different
applications today. Sanger sequencing is now used mostly for de novo initial sequencing of
a DNA molecule to obtain the primary sequence data for an organism or gene. The
relatively short ‘reads’ coming off an HTS reaction (30-400 base pairs compared to the nearly
a thousand base pair ‘reads’ from Sanger sequencing methods) make it difficult to create the
entire genome of an organism from HTS methods alone. Occasionally, Sanger sequencing is
also needed to validate the results of HTS.
On the other hand, HTS allows the use of DNA sequencing to understand single-
nucleotide polymorphisms – among the most common types of genetic variation within
a population. This becomes important in evolutionary biology as well as in the detection of
mutated genes that can result in disease. For instance, sequence variations in samples from lung
adenocarcinoma allowed the detection of rare mutations associated with the disease. The
chromatin binding sites for specific nuclear proteins can also be accurately identified using
these methods
Overall, DNA sequencing is becoming an integral part of many different applications.
Diagnostics
Genome sequencing is particularly useful for identifying the causes of rare genetic
disorders. While more than 7800 diseases are associated with a Mendelian inheritance
pattern, less than 4000 of those diseases have been definitively linked to a specific gene
or mutation. Early analysis of the exon-genome, or exome, consisting of all the expressed
genes of an organism, showed promise in identifying the causal alleles for many inherited
illnesses. In one particular case, sequencing the genome of a child suffering from a severe form
of inflammatory bowel disease connected the illness to a mutation in a gene associated with
inflammation – XIAP. While the patient initially showed multiple symptoms suggestive of an
immune deficiency, a bone marrow transplant was recommended based on the results of DNA
sequencing. The child subsequently recovered from the ailment.
In addition, HTS has been an important player in developing a greater understanding
of tumors and cancers. Understanding the genetic basis of a tumor or cancer enables doctors to
have an extra tool in their kit for making diagnostic decisions. The Cancer Genome Atlas and
International Cancer Genome Consortium have sequenced a large number of tumors and
demonstrated that these growths can vary vastly in terms of their mutational
landscape. This has also given a better understanding of the kind of treatment options that are
ideal for each patient. For instance, the sequencing of the breast cancer genome identified two
genes – BRCA1 and BRCA2 – whose pathogenic variants have an enormous impact on the
likelihood of developing breast cancer. People with some pathogenic alleles even choose to
have preventive surgeries such as double mastectomies.
Molecular Biology
DNA sequencing is now an integral part of most biological laboratories. It is used to
verify the results of cloning exercises to understand the effect of particular genes. HTS
technologies are used to study variations in the genetic compositions of plasmids, bacteria,
yeast, nematodes or even mammals used in laboratory experiments. For instance, a cell
line derived from breast cancer tissue, called HeLa, is used in many laboratories around the
world and was earlier considered as a reliable cell line representing human breast tissue. Recent
6. sequencing results have demonstrated large variations in the genome of HeLa cells from
different sources, thereby reducing their utility in cell and molecular biology.
DNA sequencing gives insight into the regulatory elements within the genome of every
cell, and the variations in their activity in different cell types and individuals. For instance, a
particular gene may be permanently turned off in some tissues, while being constitutively
expressed in others. Similarly, those with susceptibility for a specific ailment may regulate a
gene differently from those who are immune. These differences in the regulatory regions of
DNA can be demonstrated through sequencing and can give insight into the basis for
a phenotype.
Recent advances have even allowed individual laboratories to study structural
variations in the human genome – an undertaking that needed global collaboration two decades
ago.
Forensics
The ability to use low concentrations of DNA to obtain reliable sequencing reads has
been extremely useful to the forensic scientist. In particular, the potential to sequence every
DNA within a sample is attractive, especially since a crime scene often contains genetic
material from multiple people. HTS is slowly being adopted in many forensics labs for
human identification. In addition, recent advances allow forensic scientists to sequence the
exome of a person after death, especially to determine the cause of death. For instance, death
due to poisoning will show changes to the exome in affected organs. On the other hand, DNA
sequencing can also determine that the deceased had a preexisting genetic ailment or
predisposition. The challenges in this field include the development of extremely reliable
analysis software, especially since the results of HTS cannot be manually examined.