Synthetic biology is the designing of new biological systems or the modification of the existing ones that do not occur naturally. Synthetic or artificial cells organisms with minimal genomes have uses in molecular medicine, vaccines, environmental chemistry and bio-sensors. Creation of synthetic cells involve in-vitro synthesis of unitary DNA fragments of one-kilo base pairs (1kb). These unitary fragments are ligated to make ten kilo base pair (10kb) fragments, followed by tethering 10 fragments to form one hundred kilo base pair (100kb) fragments. Each step involves transformation and sequencing procedures in E. coli host cells. Ultimately, eleven of these hundred kilo base pair fragments are joined to create a “Synthetic Genome” which is maintained in yeast cells, as maximum limit of DNA transplant acceptance of E. coli is 100kb. By this approach, synthetic chromosomes can be maintained, manipulated and transplanted to an acceptor organism to create a synthetic cell. Applications of the technology include semi-synthetic approach of Artemisinic acid, which can be used to chemically synthesize anti-malarial drug Atremisinin and its therapeutically important derivatives. Second application of synthetic biology is production of meningitis vaccine against poorly immunogenic Neisseria meningitidis serogroup-B, by preparing synthetic vesicles. Third application includes disease mechanism identification of a rare-primary immunodeficiency disease “Agamaglobinemia” using reconstruction of mutant B-cell receptor components in synthetic membranes to validate a point mutation. Fourth application include environmental fixation of carbon di-oxide to produce methane by using minimal genome containing synthetic cells of Metahnococcous sp. Fifth application is production of novel biosensors which can be toggled ON and OFF using “Visible Light” as modulator. These “Gene switches” are also able to operate in mammalian cells. With potential applications and wide research domains, synthetic biology is also under ethical and religious criticism. Future of this new dimension of biological science requires scrutiny from regulatory authorities, and monetary input from funding agencies.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
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
Synthetic biology is the designing of new biological systems or the modification of the existing ones that do not occur naturally. Synthetic or artificial cells organisms with minimal genomes have uses in molecular medicine, vaccines, environmental chemistry and bio-sensors. Creation of synthetic cells involve in-vitro synthesis of unitary DNA fragments of one-kilo base pairs (1kb). These unitary fragments are ligated to make ten kilo base pair (10kb) fragments, followed by tethering 10 fragments to form one hundred kilo base pair (100kb) fragments. Each step involves transformation and sequencing procedures in E. coli host cells. Ultimately, eleven of these hundred kilo base pair fragments are joined to create a “Synthetic Genome” which is maintained in yeast cells, as maximum limit of DNA transplant acceptance of E. coli is 100kb. By this approach, synthetic chromosomes can be maintained, manipulated and transplanted to an acceptor organism to create a synthetic cell. Applications of the technology include semi-synthetic approach of Artemisinic acid, which can be used to chemically synthesize anti-malarial drug Atremisinin and its therapeutically important derivatives. Second application of synthetic biology is production of meningitis vaccine against poorly immunogenic Neisseria meningitidis serogroup-B, by preparing synthetic vesicles. Third application includes disease mechanism identification of a rare-primary immunodeficiency disease “Agamaglobinemia” using reconstruction of mutant B-cell receptor components in synthetic membranes to validate a point mutation. Fourth application include environmental fixation of carbon di-oxide to produce methane by using minimal genome containing synthetic cells of Metahnococcous sp. Fifth application is production of novel biosensors which can be toggled ON and OFF using “Visible Light” as modulator. These “Gene switches” are also able to operate in mammalian cells. With potential applications and wide research domains, synthetic biology is also under ethical and religious criticism. Future of this new dimension of biological science requires scrutiny from regulatory authorities, and monetary input from funding agencies.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
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
synthetic biology says life itself is the canvas. What might we create? we mapping our world, we are mapping every organism, we are mapping organisms that no longer exist, we are connecting all of the information but there is a problem we can’t act on much of this information yet. That is where synthetic biology comes in. so, ideas from engineering have become imposed on biology. We have come from the very basic science trying to discover genes into getting those in a microbe in developing a process, so, what if we could reprogram yeast to make medicines for us. They can be gene therapy they can be anti-cancer, antimalarials, likewise. Humans have always been good at making things. houses, furniture, gadgets of toys. But if there is one thing we have not fully explored it is to build our organisms that is what synthetic biology is all about.
in this presentation, what are the steps and strategies involved the gene cloning and i was focused only on the 1st two steps of gene cloning.they are generation of foreign DNA molecules and selection of suitable vectors.
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Cell culture based vaccine??
Cell cultures involve growing cells in a culture dish, often with a supportive growth medium. A primary cell culture consists of cells taken directly from living tissue, and may contain multiple types of cells such as fibroblasts, epithelial, and endothelial cells.
In the United States, 10 different vaccines for chicken pox, hepatitis A, polio, rabies, and rubella are cultured on aborted tissue from two fetal cell lines known as WI-38 and MRC-5. These vaccines are chicken pox, hep-A, hep-A, hep-A/hep-B, polio, rabies, rubella, measles/rubella, mumps/rubella, and MMR II (measles/mumps/rubella).
Introduction
History
Scale up in suspension:Stirred culture,Continuous flow culture,Air- lift culture,Nasa bioreactor
Scale up in monolayer culture: Roller bottle culture , multisurface culture,fixed -bed culture
Other type of culture for scaling up: HARV Vessels,STLV vessels
Monitoring of scale up
Conclusion
References
It contains information about- DNA Sequencing; History and Era sequencing; Next Generation Sequencing- Introduction, Workflow, Illumina/Solexa sequencing, Roche/454 sequencing, Ion Torrent sequencing, ABI-SOLiD sequencing; Comparison between NGS & Sangers and NGS Platforms; Advantages and Applications of NGS; Future Applications of NGS.
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Introduction
Overview
Reductionist approach
Holistic approach
What is systems biology?
○ Advantages of Systems Biology
Tools of holistic approach
○ Proteomics, Transcriptomics and Metabolomics
Conclusion
References
synthetic biology says life itself is the canvas. What might we create? we mapping our world, we are mapping every organism, we are mapping organisms that no longer exist, we are connecting all of the information but there is a problem we can’t act on much of this information yet. That is where synthetic biology comes in. so, ideas from engineering have become imposed on biology. We have come from the very basic science trying to discover genes into getting those in a microbe in developing a process, so, what if we could reprogram yeast to make medicines for us. They can be gene therapy they can be anti-cancer, antimalarials, likewise. Humans have always been good at making things. houses, furniture, gadgets of toys. But if there is one thing we have not fully explored it is to build our organisms that is what synthetic biology is all about.
in this presentation, what are the steps and strategies involved the gene cloning and i was focused only on the 1st two steps of gene cloning.they are generation of foreign DNA molecules and selection of suitable vectors.
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Cell culture based vaccine??
Cell cultures involve growing cells in a culture dish, often with a supportive growth medium. A primary cell culture consists of cells taken directly from living tissue, and may contain multiple types of cells such as fibroblasts, epithelial, and endothelial cells.
In the United States, 10 different vaccines for chicken pox, hepatitis A, polio, rabies, and rubella are cultured on aborted tissue from two fetal cell lines known as WI-38 and MRC-5. These vaccines are chicken pox, hep-A, hep-A, hep-A/hep-B, polio, rabies, rubella, measles/rubella, mumps/rubella, and MMR II (measles/mumps/rubella).
Introduction
History
Scale up in suspension:Stirred culture,Continuous flow culture,Air- lift culture,Nasa bioreactor
Scale up in monolayer culture: Roller bottle culture , multisurface culture,fixed -bed culture
Other type of culture for scaling up: HARV Vessels,STLV vessels
Monitoring of scale up
Conclusion
References
It contains information about- DNA Sequencing; History and Era sequencing; Next Generation Sequencing- Introduction, Workflow, Illumina/Solexa sequencing, Roche/454 sequencing, Ion Torrent sequencing, ABI-SOLiD sequencing; Comparison between NGS & Sangers and NGS Platforms; Advantages and Applications of NGS; Future Applications of NGS.
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Introduction
Overview
Reductionist approach
Holistic approach
What is systems biology?
○ Advantages of Systems Biology
Tools of holistic approach
○ Proteomics, Transcriptomics and Metabolomics
Conclusion
References
A Powerpoint presentation on the basics of Eicosanoids which includes Prostaglandins, Leukotrienes (LTs) ad Platelete Activating Factors (PAF) suitable for Undergraduate level Medical students.
I, Alankar an engineering graduate specialized in biotechnology. In my last year I chose this topic "Synthetic Biology" and made this presentation for my project. I gave my 100% on this Presentation.
This paper explores the complex field of synthetic biology, including its historical roots, guiding ideas, contemporary uses, and moral dilemmas raised by its groundbreaking discoveries.
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
biotechnology and its applications
application s of biotechnology, bt.cotton, cloning, dna, dna fingerprinting, dna isolation, gene manipulation, genetic engineering, goldenrice., r dnatechnology, recombinant vaccines, transgenic, vectors
This slideshow is all about Biotechnology--both traditional and modern. It also includes definitions, methods, advantages, and disadvantages of biotechnology.
This presentation is given by Miss Khunsha Fatima, Recombinant DNA Technology, its Basic Principle, Application and related topics discussed in detail watch the video for more concepts about the topic.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
2. Synthetic biology broadly refers to the use of
computer-assisted, biological engineering to design
and construct new synthetic biological parts, devices
and systems that do not exist in nature and the
redesign of existing biological organisms.
Definition
2
3. •Synthetic biology incorporates the techniques
of molecular biology.
•It differs from recombinant DNA technology in
that synthetic biology introduces synthetically
constructed parts and is not limited to the
modification of natural organisms.
•Construction of new life forms with no natural
counterpart.
3
4. Systems biology aims
to study natural biological
systems as a whole, often
with a biomedical focus
and uses simulation
and modeling tools
in comparisons
with experimental
information.
Relationship between systems biology and
synthetic biology
4
5. A key aspect of synthetic biology, which
differentiates it from genetic engineering and current
biotechnology approaches, is the application to
biology of techniques which are normally used in
engineering design and development.
The Engineering design cycle and rational
design in synthetic biology:
5
7. DNA Synthesis:
•At the most basic level, synthetic biology involves
the use synthetic DNA that was uploaded or written on
a computer and “printed” out from bottles of nucleic
acids (adenine, thymine, cytosine, and guanine—
represented by the letters A, T, C, and G).
•These DNA strands are then inserted into organisms
through a variety of genetic engineering techniques.
Differing Approaches to Synthetic Biology
7
8. “Biobricks” are standard DNA sequences that code for
certain functions.
DNA sequences can be created to make an organism
glow, for example, and engineering that biobrick into
an organism should make it glow.
These open-source “bricks” can be used by researchers
across the world to construct new genes and DNA
sequences.
Bio-bricks
8
9. Researchers, most notably Craig Venter, are
working to produce an organism or cell with the
minimum number of genes needed to survive.
One could then add any DNA sequence to this
“minimal genome or cell” and produce fuel, medicine,
or any other synthetic product.
Minimal Cell or Genome
9
11. Xenobiologists are attempting to create alternative
genetic systems such as novel nucleic acids, “suicide
genes,” or mirror biology.
11
Xenobiology
12. 12
For example, one research team has replaced thymine with 5-
chlorouracil in the genome of E. coli where others are attempting to
create “mirror” cells.
13. •Researchers are testing
combinations of inanimate
chemicals to create proto-cells,
or synthetic life without DNA.
These proto-cells would
be like truly creating life
from scratch.
13
Proto-cells
15. Fundamental techniques in synthetic
biology
There are three key technological enablers that have
facilitated the emergence and rapid development of
synthetic biology - these are:
Computational modeling
DNA sequencing
DNA synthesis. 15
16. Synthetic biology approaches the design of engineered
biological systems through the engineering cycle.
Modeling of the design, to predict system performance
prior to fabrication, is an important component of
synthetic biology.
Synthetic biology is therefore similar to systems
biology, in that both rely heavily on computer
modeling of biological processes.
16
Computational modeling
17. The ‘reading’ or sequencing of DNA is the second key
enabling technology for synthetic biology.
DNA comprises four bases. These always pair in
groups of two - T with A and G with C.
The entire content of DNA for a particular organism is
called its genome – this contains complete instructions
for constructing any type of protein, cell, tissue, organ,
etc. 17
DNA sequencing
18. •Once a genome has been sequenced, the next step
may be to 're-write', or synthesize, all or part of the
genome.
•There are a number of cases where the genome of an
organism has been entirely synthesized.
18
DNA synthesis
20. • In 2002, Cello and coworkers at State University of
New York, Stony Brook, synthesized the poliovirus
genome (7,741 bp) from its published sequence,
producing the first synthetic organism.
20
21. 21
• In 2003, the genome of
the bacteriophage ΦX-174
(5,386 bp) was assembled
in just two weeks by a team
at the J. Craig Venter
Institute.
22. Applications of synthetic biology
The ultimate goal of synthetic biology is to develop
commercial applications that will benefit society, For
example
• To design and build engineered biological systems
that process information.
22
23. Manipulate chemicals
Farnesene – an essential building block for a wide
range of chemical products (detergents, cosmetics,
perfumes and industrial lubricants and transportation
fuels) – through synthetically engineered yeast.
23
24. Engineered yeast to produce artemisinic acid an anti
malarial drug. Researchers and companies are
working on ways to produce vaccines through
synthetic microbes.
24
Maintain and enhance human health and our
environment
25. 25
Fabricate materials and structures
Re-engineering the Type III secretion system of
Salmonella typhimurium to secrete spider silk
proteins.
26. Organisms synthetically engineered to break down
biomass into sugars for fuel.
Algae naturally produces oils, but through synthetic
biology tools algae can be reengineered to produce
oils that are chemically similar or identical to the oils
that are currently used in today’s transportation and
energy infrastructure.
26
Produce energy
27. Synthetic biologists are working to replace natural
products with synthetically produced equivalents.
Synthetic production of rubber through isoprene – a
crucial building block for making artificial rubber. The
gene encoding isoprene (previously found in rubber
trees) has been synthetically engineered into E. coli to
produce isoprene. 27
Natural Product Substitutes
28. Other products currently being produced through
synthetic biology include vanilla, stevia, and palm oil
among others.
28
29. Impacts of synthetic biology on the
Conservation and Sustainable Use of
Biodiversity
Synthetic organisms threaten biological diversity if
they escape into the environment – either intentionally
or unintentionally from a lab.
29
The release of synthetic microbes:
30. Organisms are being synthetically engineered to
survive, function, and propagate in the natural
environment.
30
31. The risks synthetic biology pose to human health and
the environment are serious since synthetic biology
has the ability to create organisms that have never
existed before and their complexity will only increase
over time.
We must establish proper regulations and safeguards
before this technology evolves too far and it is too late.
31
Regulation of Synthetic Biology
sequencing is used to verify that engineered sections of DNA or possibly even whole organisms have been fabricated correctly. sequencing can also facilitate the detection and identification of novel systems and organisms.