BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
This presentation covers a general introduction to expression vector, its components, types, and its application. Then it covers some of the expression system with examples.
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
Presented by- MD JAKIR HOSSAIN
Doctoral Research Scholar
Department of Agricultural Genetic Engineering ,
Faculty of Agricultural Sciences and Technologies,
Nigde Omer Halisdemir University, Turkey
E. Mail- mjakirbotru@gmail.com
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
pBluescript is an example of a combination between plasmids and phages (phagemids).
Phagemids represent a hybrid type of class of vectors that serve to produce single-stranded DNA.
Artificial chromosome I Bacterial Artificial Chromosome I Yeast Artificial C...DevikaPatel12
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what is genetic engineering l genetic engineering explained l genetic engineering and biotechnology l Genetic engineeringl lbacterial artificial chromosome l p1 derived artificial chromosome l yeast artificial chromosome l Artificial chromosome l bacterial artificial chromosome vector l bacterial artificial chromosome vectors l bacterial artificial chromosomes l Bacterial artificial chromosome l yeast artificial chromosomes l yac l Yeast artificial chromosome
#BAC #YAC #bacterialartificialchromosome #yeastartificialchromosome #artificialchromosome #genetics #geneticengineering #DNA #dna #gene #genetherapy
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
This presentation covers a general introduction to expression vector, its components, types, and its application. Then it covers some of the expression system with examples.
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
Presented by- MD JAKIR HOSSAIN
Doctoral Research Scholar
Department of Agricultural Genetic Engineering ,
Faculty of Agricultural Sciences and Technologies,
Nigde Omer Halisdemir University, Turkey
E. Mail- mjakirbotru@gmail.com
What are an expression vector? Detailed description of plant gene structure. Plant expression vector systems are generally consists of Ri and Ti plasmids.
The other vectors which are generally used are DNA and RNA viruses.
pBluescript is an example of a combination between plasmids and phages (phagemids).
Phagemids represent a hybrid type of class of vectors that serve to produce single-stranded DNA.
Artificial chromosome I Bacterial Artificial Chromosome I Yeast Artificial C...DevikaPatel12
https://amzn.to/3Fzcqc8
https://amzn.to/3V0q6Cp
https://amzn.to/3jbtrS7
https://amzn.to/3I0A8kr
https://amzn.to/3hrJ5s8
https://amzn.to/3FZiYlu
what is genetic engineering l genetic engineering explained l genetic engineering and biotechnology l Genetic engineeringl lbacterial artificial chromosome l p1 derived artificial chromosome l yeast artificial chromosome l Artificial chromosome l bacterial artificial chromosome vector l bacterial artificial chromosome vectors l bacterial artificial chromosomes l Bacterial artificial chromosome l yeast artificial chromosomes l yac l Yeast artificial chromosome
#BAC #YAC #bacterialartificialchromosome #yeastartificialchromosome #artificialchromosome #genetics #geneticengineering #DNA #dna #gene #genetherapy
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
2. Also called genetic modification / genetic
manipulation / rDNA technology
Direct manipulation of an organism’s DNA using
biotechnology
Set of technologies used to change genetic makeup of
cells, including transfer of genes within and across
species boundaries to produce improved or novel
organisms
New DNA obtained by isolating & copying gene of
interest (GI) using rDNA methods or by artificially
synthesising DNA
5. The chosen piece of DNA is ‘cut’ from the source
organism using restriction enzymes.
The piece of DNA is ‘pasted’ into a vector and the ends
of the DNA are joined with the vector DNA by ligation.
The vector is introduced into a host cell, by a process
called transformation. The host cells copy the vector
DNA along with their own DNA, creating multiple
copies of the inserted DNA.
The vector DNA is isolated from the host cells’ DNA
and purified.
6.
7. Nucleic acid molecules capable of autonomous
replication, can carry a gene and deliver it into a cell
Different types of vectors includes :
Plasmids
Bacteriophages
Cosmids
Phagemids
Artificial Chromosomes (BAC, YAC, HAC, MAC, Plant
derived AC)
8. Synthetic chromosomes consisting of fragments of
DNA integrated into a host chromosome- introduced
into host cells to propagate and used to transfect
other cells, introducing new DNA.
Useful in cloning larger fragments of DNA, as plasmids
can only contain up to 10,000 base pairs and phages
are hard to work with.
Contain 300,000(BAC) to 1,000,000(YAC) base pairs-
reduces amount of runs needed for a large fragment
to be analyzed-easier and quicker to clone and
transform genes
9. Linear or Circular
Different types
Bacterial Artificial Chromosome (BAC)
Yeast Artificial Chromosome (YAC)
P1 derived Artificial Chromosome (PAC)
Mammalian Artificial Chromosome (MAC)
Human Artificial Chromosome (HAC)
YAC – Cloning in yeast
BAC & PAC – Bacteria
MAC & HAC – Mammalian & Human cells.
10. Developed by Mel Simmons and coworkers in 1992
1st BAC vector – PBAC108L
Plasmids constructed with replication origin of E.coli F
factor, so can be maintained in a single copy per cell
Can hold DNA fragments of 75 to 300 kb
Recombinant BACs introduced into E.coli by
electroporation
Then rBAC replicates like an F factor
11. Components :
ori : origin of replication
repE : for plasmid replication
and regulation of copy number
parA and parB : for partitioning
F plasmids to daughter cells
during division and ensures
stable maintenance of the BAC
Selectable marker for antibiotic
resistance. Some BACs also
have lacZ at cloning site
for blue/white selection
T7 & Sp6 phage promoters for
transcription of inserted genes.
12.
13. Stable inserts and do not delete sequences
Easy to manipulate
Transforming efficiency higher than that of YAC
Speedy growth of E.coli host
Simpler to purify
More user friendly
Helpful in development of vaccines
14. • Fragment DNA contains unrelated genes may lead to
indirect, non-specific gene expression and
unanticipated changes in the cell phenotype.
• Generation and screening of recombinant BAC
constructs can be time-consuming and labor-intensive.
• Oversized BAC DNA constructs are more easily sheared
and degraded during manipulation before
transfection.
• Random recombination events may occur.
• Intra molecular rearrangements - reduce the
recombination efficiency and increase the rate of false
positive clones in some selection/counter-selection
approaches
15. The P1 derived artificial chromosome (PAC) are DNA
constructs that are derived from the DNA of P1
bacteriophage. They can carry large amounts (about
100-300 kb) 0f other sequences for a variety of
bioengineering purposes.
Host cell – E.coli
16. Devised and first reported in 1987 by David Burk and
Olson
pYAC3- first YAC developed.
Special linear DNA vectors that resemble normal yeast
chromosome
Circular double stranded DNA - contains a replication
origin (colE 1) compatible with E. coli in addition to
yeast replication origin or an yeast ARS element-useful
for amplification of the vector in E. coli.
Clone large DNA segment (100 – 1000kb)
17. By inserting large fragments of DNA, inserted
sequences can be cloned and physically mapped using
a process called chromosome walking.
Initially used for the Human Genome Project- due to
stability issues abandoned for the use of Bacterial
Artificial Chromosome.
18. Primary components -
autonomously replicating
sequence (ARS),
centromere (CEN) and
telomeres (TEL) from S.
cerevisiae.
Selectable marker genes,
such as antibiotic
resistance and a visible
marker - select
transformed yeast cells.
19. A YAC is built using an initial circular DNA plasmid,
cut into a linear DNA molecule using restriction
enzymes; DNA ligase is then used to ligate a DNA
sequence or gene of interest into the linearized
DNA, forming a single large, circular piece of DNA.
20.
21. Generating whole DNA libraries of the genomes of
higher organisms
YAC clones used as hybridization probes for the
screening of cDNA libraries
Study of regulation of gene expression by cis-acting,
regulatory DNA elements after the transfer of these
YACs from yeast to mammalian cells
Used for isolation of functionally analogous
mammalian DNA sequences in order to develop MACs
Main difficulty in constructing MAC using YAC is isolation and
maintenance of mammalian centromere due to its large size and high
instability in yeast cell
22. Very large DNA molecules are very fragile and prone to
breakage, leading to problem of rearrangement.
High rate of loss of the entire YAC during mitotic
growth.
Difficult to separate YAC from the other host
chromosomes because of their similar size.
Separation requires sophisticated pulse-field gel
electrophoresis (PFGE).
Yield of DNA is not high when YAC is isolated from
yeast cells.
Clones tend to be unstable, with their foreign DNA
inserts often being deleted.
23. Mammalian artificial chromosomes (MACs) are
conceptually similar to YACs, but instead of yeast
sequences they contain mammalian or human ones
Like YACs rely on the presence of centromeric and
telomeric sequences and origin of DNA replication
Involve autonomous replication and segregation in
mammalian cells, as opposed to random integration
into chromosomes (as for other vectors)
Can be modified for their use as expression systems of
large genes, including not only the coding region but
can contain control elements
24. Two principal procedures exist for the generation of
MACs.
1) In one method, telomere-directed fragmentation of
natural chromosomes is used. For example, a human
artificial chromosome (HAC) has been derived from
chromosome 21 using this method.
2) Another method involves de novo assembly of cloned
centromeric, telomeric, and replication origins in vitro .
25. MAC vectors are difficult to assemble as compared to
YAC vectors
Mammalian DNA has higher degree of repetition and
larger centromere and telomere regions
Also the sequences necessary for chromosome
replication in mammalian system are not well defined
till now
MAC vectors have application in the field of gene
therapy and eukaryotic protein expression and
production.
26. Developed by Harrington et al., in 1997
synthetically produced vector DNA, possessing
characters of human chromosome
micro chromosome that can act as a new chromosome
in a population of human cells
instead of 46 chromosomes, the cell could have 47
with 47th being very small
Size 1/10th to 1/5th of human chromosome -6 – 10
megabases (Mb)
27. able to carry new genes introduced by human
researchers
researchers could integrate different genes that
perform a variety of functions, including disease
defence
Using its own self-replicating and segregating systems,
HAC can behave as a stable chromosome that is
independent from the chromosomes of host cells
Mitotically stable up to 6 months
28. COMPONENTS:
Replication origin from which DNA duplication begins
Centromere – functions in proper chromosome
segregation during cell division
Telomere – protects ends of linear chromosomes
30. Human chromosome transferred to chicken DT40 cells.
Targeting linearized vectors containing telomeric
repeats, a selectable marker and sequences
homologous to q and p arms of chromosome
transected to chicken cells.
Recombinational interaction between targeting
vectors and targeted sites at chromosome - forms new
telomeres - truncation of distal chromosomal arms.
HAC generated by subsequent truncation of p-and q-
arms of chromosome.
Usually a gene-loading loxP cassette is included into
HAC during chromosome truncation (i.e., included into
one of the targeting vectors).
31. Final HAC vector transferred into Chinese hamster
ovary (CHO) cells. In CHO cells, a desired gene loaded
into loxP site of HAC by Cre/loxP-mediated
recombination
From CHO cells, HAC with a gene of interest
transferred to desired recipient cells via a microcell-
mediated transfer technique.
32.
33. In de novo artificial chromosome by a bottom down
approach, exogenous chromosomes can be circular or
linear, created de novo from cloned chromosomal
components, either naturally occurring or synthetic
high – order α-satellite DNA arrays introduced on BAC,
YAC, or P1 artificial chromosome vectors, which have a
functional centromere and autonomously replicate
and segregate.
34. Useful in expression studies as gene transfer vectors,
as a tool for elucidating human chromosome function
Used to create transgenic animals to use as animal
models of human disease and for production of
therapeutic products
Can carry genes to be introduced into the cells in gene
therapy
Can carry human genes that are too long
35. Type Transgene
capacity
Host cell Advantages Disadvantages
BAC/PAC Up to 300 kb E.Coli Can be infectiously
delivered
Ease of purification
and modification .
Medium transgene
capacity.
May be
immunogenic
Difficult to
chemically
transduce cells
YAC Up to 2.5 mb Yeast Large transgene
capacity
Ease to production
and modification
Fragile construct
Low transduction
efficiency
HAC Unlimited Cultured
human
cells
Large transgene
capacity
Naturally segregates
in human cells
Non-immunogenic
Non-integrating
Fragile construct
Difficult to purify
Low transduction
efficiency
36. PACs are chromosome-based vectors
(minichromosomes) for genetic engineering
Mini-chromosome
• Vector for plant artificial chromosome.
• Properties
1. No genes of their own, can be used as a super vector
to express foreign gene, minimum interference with
the host growth and development.
2. Stable during mitosis and meiosis, allow the foreign
gene to be faithfully expressed and transmitted.
3. Allow addition deletion and replacement of genes
with recent – genome editing technology.
37. Requirements for plant artificial
chromosome(mini chromosome)
1. Centromere
2. Telomere
3. Sufficient chromatin
4. Selectable marker transgene
5. Site specific recombination system
38. • Two methods
1. Essential components are assembly the gene outside
the plant cell, then transfer them into a plant cell.
But it creates more complexity to use.
39. 2. Mini chromosome constructed by telomere-mediated
chromosomal truncation(TMCT).
• Transformation of telomere –containing sequences
into genome, new telomeres at the site of integration.
• It must have functional centromere to keep stable
during cell division.
40. The selectable marker gene(SMG) and the gene of
interest (GOI) in particular mini chromosome were
removed and replaced by those on donor plasmid
using specifically added restriction site on the mini
chromosome and homologous recombination.
41. • PACs after being generated in plants, cloned in-vitro
and transferred back into plants of the same species
they were generated in.
• Insertion is by protoplast fusion.
• To overcome the species specificity, allowing insertion
into alien species.
42. Unlimited number of gene can be integrated and
expressed.
Avoids linkage drag when transgene transferred to
other germplasm in breeding
Prevents disruption of endogenous gene function.
A minichromosome is a small chromatin-like structure consisting of centromeres, telomeres and replication origins[1] and little additional genetic material. They replicate autonomously in the cell during cellular division. The origin of minichromosomes is the result of natural processes (chromosomal aberrations) or genetic engineering.
A. Engineering of human artificial chromosome via top--down approach. As the first step, a human chromosome is transferred to homologous recombination-proficient chicken DT40 cells(Avian leukosis virus induced bursal lymphoma cell line derived from a chicken). The targeting linearized vectors containing human telomeric repeats (red arrow), a selectable marker and sequences homologous to the q-and p-arms(long and short arms of chromosome)of the chromosome (blue and green boxes) are transected into the chicken cells. Recombinational interaction between the targeting vectors and targeted sites at the chromosome seeds the formation of new telomeres, thereby truncating (Telomeres are highly repetitive sequences at the ends of chromosomes that act as protection structure for chromosome stability. The integration of telomere sequences into the genome by genetic transformation can create chromosome instability because the integrated telomere sequences tend to form de novo telomeres at the site of integration. Thus, telomere repeats can be used to generate minichromosomes by telomere-mediated chromosome truncation in both plants and animals )the distal portion of chromosomal arms. The Human artificial chromosome (HAC) is generated by subsequent truncation of the p-and q-arms of the chromosome. Usually a gene-loading loxP cassette is included into the HAC during the chromosome truncation (i.e., included into one of the targeting vectors). Then the final HAC vector is transferred into Chinese hamster ovary (CHO) (hprt -/-) cells. In CHO cells, a desired gene can be loaded into the loxP site of HAC by Cre/loxP-mediated recombination. From CHO cells, the HAC with a gene of interest can be transferred to desired recipient cells via a microcell-mediated transfer technique(used to transfer a chromosome from a defined donor cell into a recipient cell line) for further gene complementation assays.