This document summarizes the development of Golden Rice, a genetically engineered rice variety that produces beta-carotene, a precursor of vitamin A. It was developed to address vitamin A deficiency in developing countries where rice is a staple crop. The document describes how researchers introduced genes from daffodil and bacteria to complete the beta-carotene biosynthesis pathway in rice endosperm. Early research demonstrated beta-carotene production in transgenic rice. Further work improved beta-carotene levels and introduced the trait into indica rice varieties commonly consumed in Asia where vitamin A deficiency is widespread. The goal of Golden Rice is to provide a sustainable solution to prevent blindness and other health issues caused by vitamin A deficiency.
An overview of the Agrobacterium-mediated gene transfer process. Moreover, studied different kinds of Agrobacterium species are involved in this mechanism.
Agrobacterium is a rod-shaped, Gram-negative bacteria found mostly in the soil. It is a plant pathogen that is responsible for causing crown gall disease in them. This bacteria is also known as the natural genetic engineer because of it's the ability to integrate its plasmid Gene into the plant genome.
Agrobacterium tumefaciens transfer of their genetic material T-DNA of Ti-plasmid into the plant cell: A: Agrobacterium tumefaciens; B: Agrobacterium genome; C: Ti Plasmid : a: T-DNA , b: Vir genes , c: Replication origin , d: Opines catabolism genes; D: Plant cell
A Ti-Plasmid (tumor-inducing plasmid) is a ds, circular DNA that often, but not always. It's a piece of genetic equipment that transfers genetic material from bacterial cells means Agrobacterium tumefaciens into plant cells used to induce tumors in the plant. The Ti-plasmid is damage when Agrobacterium is grown above 28 °C. Such cured bacteria don't induce crown gall disease in the plant due to they are avirulent. The Ti-Plasmid are classified into two types on the basis of opine genes are present in T-DNA.
The Plasmid has 196 genes that code for 195 proteins. There is no one structural RNA. The plasmid is 206.479 nucleotides long. the GC content is 56% and 81% of the genetic material is coding genes.
The modification of this plasmid is a very important source in the production of transgenic plants.
The T-DNA must be cut out of the circular plasmid. A VirD1/D2 complex nicks the DNA at the left and right border sequences. The VirD2 protein is covalently attached to the 5' end. VirD2 contains a motif that leads to the nucleoprotein complex being targeted to the type IV secretion system (T4SS).
In the cytoplasm of the recipient cell, the T-DNA complex becomes coated with VirE2 proteins, which are exported through the T4SS independently from the T-DNA complex. Nuclear localization signals, or NLS, located on the VirE2 and VirD2 are recognized by the importin alpha protein, which then associates with importin beta and the nuclear pore complex to transfer the T-DNA into the nucleus. So that the T-DNA can integrate into the host genome.
We inoculate Agrobacterium containing our genes of interest, onto wounded plant tissue explants. The Agrobacterium then transfers the gene of interest into the DNA of the plant tissue.
Somaclonal Variation in Plant tissue culture - Variation in somaclones (somatic cells of plants)
Somaclonal variation # Basis of somaclonal variation # General feature of Somaclonal variations # Types and causes of somaclonal variation # Isolation procedure of somaclones via without in-vitro method and with in-vitro method with their limitations and advantages # Detection of isolated somaclonal variation # Application (with examples respectively related to crop improvement) # Advantages and disadvantages of somaclonal variations.
https://www.youtube.com/watch?v=IZwrkgADM3I
Also watch, Gametoclonal variation slides to understand, how to changes occur in gametoclones of plants.
https://www.slideshare.net/SharmasClasses/gametoclonal-variation
The different types of external stresses that influence the plant growth and development.
These stresses are grouped based on their characters
Biotic
Abiotic
Almost all the stresses, either directly or indirectly, lead to the production of reactive oxygen species (ROS) that create oxidative stress in plants.
This damages the cellular constituents of plants which are associated with a reduction in plant yield.
An overview of the Agrobacterium-mediated gene transfer process. Moreover, studied different kinds of Agrobacterium species are involved in this mechanism.
Agrobacterium is a rod-shaped, Gram-negative bacteria found mostly in the soil. It is a plant pathogen that is responsible for causing crown gall disease in them. This bacteria is also known as the natural genetic engineer because of it's the ability to integrate its plasmid Gene into the plant genome.
Agrobacterium tumefaciens transfer of their genetic material T-DNA of Ti-plasmid into the plant cell: A: Agrobacterium tumefaciens; B: Agrobacterium genome; C: Ti Plasmid : a: T-DNA , b: Vir genes , c: Replication origin , d: Opines catabolism genes; D: Plant cell
A Ti-Plasmid (tumor-inducing plasmid) is a ds, circular DNA that often, but not always. It's a piece of genetic equipment that transfers genetic material from bacterial cells means Agrobacterium tumefaciens into plant cells used to induce tumors in the plant. The Ti-plasmid is damage when Agrobacterium is grown above 28 °C. Such cured bacteria don't induce crown gall disease in the plant due to they are avirulent. The Ti-Plasmid are classified into two types on the basis of opine genes are present in T-DNA.
The Plasmid has 196 genes that code for 195 proteins. There is no one structural RNA. The plasmid is 206.479 nucleotides long. the GC content is 56% and 81% of the genetic material is coding genes.
The modification of this plasmid is a very important source in the production of transgenic plants.
The T-DNA must be cut out of the circular plasmid. A VirD1/D2 complex nicks the DNA at the left and right border sequences. The VirD2 protein is covalently attached to the 5' end. VirD2 contains a motif that leads to the nucleoprotein complex being targeted to the type IV secretion system (T4SS).
In the cytoplasm of the recipient cell, the T-DNA complex becomes coated with VirE2 proteins, which are exported through the T4SS independently from the T-DNA complex. Nuclear localization signals, or NLS, located on the VirE2 and VirD2 are recognized by the importin alpha protein, which then associates with importin beta and the nuclear pore complex to transfer the T-DNA into the nucleus. So that the T-DNA can integrate into the host genome.
We inoculate Agrobacterium containing our genes of interest, onto wounded plant tissue explants. The Agrobacterium then transfers the gene of interest into the DNA of the plant tissue.
Somaclonal Variation in Plant tissue culture - Variation in somaclones (somatic cells of plants)
Somaclonal variation # Basis of somaclonal variation # General feature of Somaclonal variations # Types and causes of somaclonal variation # Isolation procedure of somaclones via without in-vitro method and with in-vitro method with their limitations and advantages # Detection of isolated somaclonal variation # Application (with examples respectively related to crop improvement) # Advantages and disadvantages of somaclonal variations.
https://www.youtube.com/watch?v=IZwrkgADM3I
Also watch, Gametoclonal variation slides to understand, how to changes occur in gametoclones of plants.
https://www.slideshare.net/SharmasClasses/gametoclonal-variation
The different types of external stresses that influence the plant growth and development.
These stresses are grouped based on their characters
Biotic
Abiotic
Almost all the stresses, either directly or indirectly, lead to the production of reactive oxygen species (ROS) that create oxidative stress in plants.
This damages the cellular constituents of plants which are associated with a reduction in plant yield.
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
The presentation gives overview of production of secondary metabolites using callus culture as well as tissue culture techniques. Various batch and continuous culturing process are described on the basis of secondary metabolite to be synthesised.
☺INTRODUCTION
☺Bt COTTON
☺MAJOR PESTS OF COTTON
☺MODE OF ACTION OF Bt GENE
☺ADVANTAGES
☺DISADVANTAGES
☺CONCLUSION
☺REFERENCES
Genetically modified variety of cotton that produces an insecticide whose gene has been derived from a soil bacterium called Bacillus thuringiensis (Bt).
Three types of toxins.
A total of 229 cry toxins ( cry1Aa to Cry72Aa), cyt toxins ( cyt 11Aa to cyt3Aa) and 102 vip toxins( vip1Aa1 to vip4Aa1) have been discovered.
This presentation focus on how can be develop of herbicides resistant plants, Role of herbicides resistant plant, action of herbicides in unusual plants and agronomic importance of herbicides resistant plants.
Don"t forget to like, share and download
Introduction
Definition of an Insect Resistant Plant
What is the Bt gene?
History
The crystal ( cry)Proteins
Definition of cry protein
How does Bt work?
Mechanism of Bt toxicity
Mode of Action of Insecticidal Crystal Protein
Bt Technology
The Insect Resistance Problem
Advantages
Limitations
Conclusion
References
1.What is plant tissue culture?
2.Production of virus free plants.
3.History.
4.Virus elimination by heat treatment.
5.Virus elimination by Meristem Tip culture.
6.Factor affecting virus eradication by Meristem Tip culture.
7.Chemotherapy.
8.Virus elimination through in vitro shoot-tip Grafting.
9.Virus Indexing.
10.Conclusion .
11.References .
this presentation deals with Molecular Ph(f)arming, and bio-safety issues related to it. This was presented by me in credit seminar in the division of Agricultural physics, IARI, New Delhi.
the sources used are duly acknowledged in the figures and slides.
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
The presentation gives overview of production of secondary metabolites using callus culture as well as tissue culture techniques. Various batch and continuous culturing process are described on the basis of secondary metabolite to be synthesised.
☺INTRODUCTION
☺Bt COTTON
☺MAJOR PESTS OF COTTON
☺MODE OF ACTION OF Bt GENE
☺ADVANTAGES
☺DISADVANTAGES
☺CONCLUSION
☺REFERENCES
Genetically modified variety of cotton that produces an insecticide whose gene has been derived from a soil bacterium called Bacillus thuringiensis (Bt).
Three types of toxins.
A total of 229 cry toxins ( cry1Aa to Cry72Aa), cyt toxins ( cyt 11Aa to cyt3Aa) and 102 vip toxins( vip1Aa1 to vip4Aa1) have been discovered.
This presentation focus on how can be develop of herbicides resistant plants, Role of herbicides resistant plant, action of herbicides in unusual plants and agronomic importance of herbicides resistant plants.
Don"t forget to like, share and download
Introduction
Definition of an Insect Resistant Plant
What is the Bt gene?
History
The crystal ( cry)Proteins
Definition of cry protein
How does Bt work?
Mechanism of Bt toxicity
Mode of Action of Insecticidal Crystal Protein
Bt Technology
The Insect Resistance Problem
Advantages
Limitations
Conclusion
References
1.What is plant tissue culture?
2.Production of virus free plants.
3.History.
4.Virus elimination by heat treatment.
5.Virus elimination by Meristem Tip culture.
6.Factor affecting virus eradication by Meristem Tip culture.
7.Chemotherapy.
8.Virus elimination through in vitro shoot-tip Grafting.
9.Virus Indexing.
10.Conclusion .
11.References .
this presentation deals with Molecular Ph(f)arming, and bio-safety issues related to it. This was presented by me in credit seminar in the division of Agricultural physics, IARI, New Delhi.
the sources used are duly acknowledged in the figures and slides.
Introduction: Biotechnology is an emerging field of research as it has the potential to solve many biological problems which could not be solved till now with conventional techniques.
The use of biology to develop technologies and products for the welfare of human beings is known as Biotechnology. It has various applications in different fields such as Therapeutics, Diagnostics, Processed Food, Waste Management, Energy Production, Genetically Modified Crops etc.
Biotechnology means 'applications of scientific and engineering principles to biological processes to provide goods and services'. Full understanding of biological processes is possible with detailed analysis of gene structure and function i.e. the Genetic Engineering means the introduction of manipulated genetic material (DNA) into a cell in such a way as to replicate and be passed on to progeny cells'. The outcome is attractive and promising.
A description of the history, variation in methods/ approaches for biofortifying rice, benefits and challenges faced with biofortified rice and consequences for future generations..
Golden rice is a variety of rice (Oryza sativa) produced through genetic engineering to biosynthesize beta-carotene, a precursor of vitamin A, in the edible parts of rice.It is intended to produce a fortified food to be grown and consumed in areas with a shortage of dietary vitamin A, a deficiency which each year is estimated to kill 670,000 children under the age of 5 and cause an additional 500,000 cases of irreversible childhood blindness. Rice is a staple food crop for over half of the world's population, providing 30–72% of the energy intake for people in Asian countries, and becoming an effective crop for targeting vitamin deficiencies.
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.
(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.
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 entangled aventures in wonderlandRichard 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.
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.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
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.
3. Millions could be saved, if only ...
GM technology could help tackle
both poverty and health problems
facing developing countries — if
only those who oppose GM crops
would relax their stance and weigh
up the technology's costs and
benefits.
5. Why Rice?
• Global staple food and is especially
important in asia.
• Cultivated for over 10,000 years.
• Rice provides as much as 80 percent or
more of the daily caloric intake of 3 billion
people, which is half the world’s
population.
• To provide pro-vitamin A to third world i.e,
developing countries where malnutrition
and vitamin A deficiency are common.
6. • It is generally consumed in its milled form with outer layers
removed (Ye et al., 2000; Beyer et al., 2002).
• The main reason for milling is to remove the oil-rich aleurone
layer, which turns rancid upon storage.
• As a result, the edible part of rice grains consists of the
endosperm, filled with starch granules and protein bodies, but it
lacks several essential nutrients such as carotenoids exhibiting
provitamin A-activity.
• Vitamin A deficiency is a serious health
problem in at least 26 countries in Asia,
Africa and Latin America (Beyer et al.,
2002).
7. Who Began the Golden Rice Project?
The scientific details of the rice were first published in Science
(287:303-5, 2000), the product of an eight-year project by Ingo
Potrykus of the Swiss Federal Institute of Technology and Peter
Beyer of the University of Freiburg.
The Golden Rice Humanitarian Board encourages further
research to determine how the technology may play a part in the
ongoing global effort to fight VAD in poor countries.
8. inspiring to scientists all over the world…….
Funded by the Rockefeller Foundation, the Swiss Federal
Institute of Technology.
Syngenta, a crop protection company.
9. Golden Rice, the real thing
• Golden rice is a variety of Oryza sativa rice produced through genetic
engineering to biosynthesize beta-carotene, a precursor of vitamin A, in the
edible parts (endosperm) of rice.
• Vitamin A deficiency causes blindness among children and may even
lead to death.
According to the WHO, dietary vitamin A deficiency (VAD) causes some
250,000 to 500,000 children to go blind each year as a result of
xerophthalmia and keratomalacia.
• The US Recommended Daily Allowance (RDA) for vitamin A is 400µg
retinol/day for children aged 1-3 years and 800µg for adults.
10. Golden Rice – A golden opportunity?
• Vitamin A deficiency often occurs where rice is the staple food since rice
grain does not contain provitamin A i.e., β-carotene.
•Rice produces β-carotene in the leaves but not in the grain, where the
biosynthetic pathway is turned off during plant development.
•The resulting transgenic rice ‘golden rice’ contains good quantities of β-
carotene, which gives the grain a golden colour.
indicator of β-carotene concentration
11. Happy farmers, hungrier planet?
It has been shown that between 23 and 34 percent of child
mortality could be prevented by having a universal source of
vitamin A
Mothers about 40 percent of maternal mortality could be
prevented
12. Genetic engineering was the only way to produce GR
(‘Breeding where possible
Genetic modification where necessary‘)
there is no rice germplasm capable of synthesizing carotenoids
in the germplasm available.
Transgenic approach has become feasible during recent years
due to two reasons:
1. The rapid progress in the development of rice transformation
technologies through biolistic methods as well as using
Agrobacterium.
2. The availability of almost complete molecular elucidation of the
carotenoid biosynthetic pathway in numerous bacteria and plants
which provides ample choice of bacterial genes and plant cDNA
to select from.
13. Growers can reuse their seed as they please
Golden Rice offers people in developing countries a valuable and
affordable choice in the fight against the scourge of malnutrition.
A 2009 study of boiled golden rice fed to volunteers concluded that
golden rice is effectively converted into vitamin A in humans and a
2012 study of golden rice that fed 68 children ages 6 to 8, and
concluded that the golden rice was as good as vitamin A
supplements and better than the natural beta-carotene in spinach
(Tang et al., 2009).
14. The Science of Golden Rice
• Biosynthetic pathway of provitamin A is a continuation of
lycopene pathway.
• Immature rice endosperm is capable of synthesizing GGDP
(geranyl geranyl diphosphate) but subsequent stages of
pathway are not expressed in this tissue.
• The exogenous lyc gene has a transit peptide sequence
attached so it is targeted to the plastid, where geranyl geranyl
diphosphate formation occurs.
15. How does it work?
• The addition of 3 genes in the rice genome will complete the
biosynthetic pathway.
Phytoene synthase (psy) gene –derived from daffodils (Narcissus
pseudonarcissus)
fused to rice endosperm-specific glutelin (Gt1) promoter
• (Phytoene synthase is a transferase enzyme involved in the
biosynthes of carotenoids. It catalyzes the conversion of geranyl
geranyl pyrophosphate to phytoene).
Three steps required to convert : phtoene to β-carotene
Phytoene desaturase (pds) and ζ-carotene desaturase
to introduce double bonds to form lycopene.
16. Lycopene cyclase – from soil bacteria Erwinia uredovora
form rings in the beta-carotene (biosynthesis of carotenoids in the
endosperm).
Bacterial carotene desaturase capable of introducing all four
double bonds can be substituted for the Phytoene desaturase and
ζ-carotene desaturase.
Manipulation of Golden rice would require the introduction of 3
genes :
Phtoene synthase, Carotene desaturase, Lycopene beta-cyclase.
The daffodil psy gene rice glutelin promoter construct was inserted
into the vector pZPsC, along with the bacterial carotene desaturase
gene, (crt1) controlled by the 35S promoter.
17. Both enzymes were targeted to the plastid (the site of GGDP
synthesis): psy gene by its own transit peptide and the crt1 gene by
fusion to a pea ribulose-1,5-bisphosphate carboxlase/oxygenase
small subunit (rbcs) transit peptide sequence.
The lycopene β-cyclase gene with a functional transit peptide was
inserted into vector pZLcyH under the rice endosperm-specific
glutelin promoter along with hygromycin resistance marker gene.
(a) pZPsc
(b) pZLcyH
18. (c) pB19hpc
The three vectors constructed. pB19hpc is used in single transformation whereas
pZPsC and pZLcyH are used in co-transformation. LB, left borders; RB, right
borders; p, promoter; Gt1 glutelin; psy, phytoene synthase; crtl, bacterial carotene
desaturase; lcy, lycopene β-cyclase; aphIV, hygromycin resistant gene. These
three vectors were then spliced into a T-DNA vector for transformation
experiments. (Beyer et al., 2002).
Co-transformation
500 precultured immature embryos were inoculated with an
Agrobacterium mixture of LBA4404/pZCycH and LBA4404/pZLcyH
(Ye et al., 2000; Beyer et al., 2002).
The co-transformed plants were analyzed by Southern
hybridization (Ye et al., 2000; Beyer 2002).
19. • The presence of pZPsC was analyzed by restriction digestion (Ye
et al., 2000).
• To determine the formation of β-carotene, mature seeds from the
transform lines and control plants were air dried, de-husked and
polished with emery paper (Ye et al., 2000; Beyer et al., 2002).
The colour of the transformed endosperms was observed (Ye et
al., 2000; Beyer et al., 2002).
Single Transformation
• 800 rice immature embryos were inoculated with Agrobacterium
LBA 4404/pB19hpc with the presence of hygromycin (Ye et al.,
2000; Beyer et al., 2002).
20. • The hygromycin-resistance plants were analyzed by Southern
hybridization for the presence of psy and crtl genes (Ye et al.,
2000; Beyer et al., 2002).
• The endosperm of these plants' seeds were isolated and
appeared yellow, indicating carotenoid production (Ye et al.,
2000).
• High Performance Liquid Chromatography (HPLC) analysis
revealed the presence of β-carotene in transgenic endosperm
(Beyer et al., 2002).
21. -Carotene Pathway Problem in Plants
IPP
Geranylgeranyl diphosphate
Phytoene
Lycopene
-carotene
(vitamin A precursor)
Phytoene synthase
Phytoene desaturase
Lycopene-beta-cyclase
ξ-carotene desaturase
Problem:
Rice lacks
these enzymes
Normal
Vitamin A
“Deficient”
Rice
22. The Golden Rice Solution
IPP
Geranylgeranyl diphosphate
Phytoene
Lycopene
-carotene
(vitamin A precursor)
Phytoene synthase
Phytoene desaturase
Lycopene-beta-cyclase
ξ-carotene desaturase
Daffodil gene
Single bacterial gene crtI;
performs both functions
Daffodil gene
-Carotene Pathway Genes Added
Vitamin A
Pathway
is complete
and functional
Golden
Rice
23. • In one transgenic line, β-carotene content was as high as 85%
of the total carotenoids present in the grain.
• One explanation is that enzymes downstream along the
pathway, such as lycopene cyclases (lyc) and alpha- and beta-
carotene hydroxylases (hyd) are still being produced in non-
transformed rice endosperm, while psy and phytoene
desaturase (pds) and ζ-carotene desaturase (zds) are not.
• Synthesis of lycopene by psy and crt1 in transgenic plants
provides the substrate for these downstream enzymes.
24. The fact that a psy transgene alone led to phytoene accumulation but
not to desaturated products (Burkhardt et al., 1997) is evidence for
the absence of at least one active desaturase, namely pds.
Similarly, the expression of crtI alone did not produce any colour in
rice endosperm, because of the lack of psy activity.
25. Why do you think that Potrykus and his
co-workers initially used the less
effective biolistic transformation
method?
Rice is a monocot, and till then, the A. tumefaciens
method was restricted for use with dicots.
26. Improvements made to Golden rice
• The pmi (phosphomannose isomerase or mannose 6-phosphate
isomerase) mannose-selection gene was substituted to avoid
antibiotic selection using the hygromycin-resistance gene.
• The golden Rice trait was genetically engineered into indica rice
cultivars. Indica rice is consumed by 90% of the Asian
population, whereas the original Golden Rice was produced
using the japonica variety Taipei 309.
• Subsequent research indicated that the lycopene beta-cyclase
transgene was not required to produce beta carotene in the
endosperm.
27. A new Golden Rice generation
Golden Rice 2
Further work by Syngenta to optimize beta-carotene production showed
that the daffodil phytoene synthase was rate limiting and psy gene from
maize was much more effective (resulting in the greatest accumulation of
total carotenoids and -carotene)
After trying with psy genes from different sources it turned out that the
maize and rice genes gave the best results (Paine et al., 2005).
In the process, Golden Rice lines were obtained that accumulated up
to 37 μg/g carotenoids, of which 31 µg/g was β-carotene (as compared
to the first generation Golden Rice (original golden rice was called GR1)
where only 1.6 μg/g were obtained.
28. • Transformation of rice with the construct pSYN12424 resulted in
a 23 fold increase in carotenoids compared with the original
Golden Rice and has been named Golden Rice 2.
• To construct Golden Rice 2, the phytoene synthase gene (psy)
from maize and the carotene desaturase gene (crtI) from
Erwinia uredovora were inserted into rice.
Gt1p, crtI, nos, Zea mays phytoene synthase (psy), Zea mays
polyubiquitin Ubi–1 promoter with intron, E. Coli phospho-mannose
isomerase (pmi) selectable marker.
29. In 2006, Stein, for India, finds that the newer GR would reduce the
burden of VAD in India by 5-54%, depending upon assumptions
about adoption and who consumes it.
Although some beta-carotene is destroyed during cooking and not
all of it is absorbed into the body, the level of beta-carotene in
Golden Rice 2 is comfortably enough to prevent VAD in people
eating ordinary amounts of rice.
30. GR2 GR1
Wild-Type
Tiny grain with a giant footprint
The image clearly shows the progress made since the proof-of-concept stage of
Golden Rice. The new generation, also known as GR2 contains β-carotene levels
that will allow to provide an adequate amount of provitamin A in for children's diets in
SE Asia.
31. Cons behind ‘magic rice ’
Greenpeace and associated GMO opponents regard “golden
rice” as a “Trojan horse” that may open the route for other GMO
applications.
Health
By promoting GE rice you encourage a diet based on one staple
rather than an increase in access to the many vitamin-rich food
plants. These plants would address a wide variety of
micronutrient deficiencies, not just VAD.
GE crops (including GE rice) have the potential to cause allergic
reactions.
Supply does not provide a substantial quantity as the
recommended daily intake.
32. • Environment
Loss of Biodiversity. May become a gregarious weed and
endanger the existence of natural rice plants.
Genetic contamination of natural, global staple foods.
• Culture
Some people prefer to cultivate and eat only white rice based
on traditional values and spiritual beliefs.
• Financial interest
The majority of patents for genetically engineered plants are held
by a few large multinational companies. So it's in their financial
interest – and not ours, the public – to get us hooked on their
seed
33. Improve level of IRON AND ZINC in Rice grains
Iron deficiency is the most widespread micronutrient deficiency
world-wide.
Affecting an estimated one-third of the world’s population and
causing 0.8 million deaths annually worldwide.
Anemia caused by iron deficiency triggers serious disorders such
as abortion, brain damage in infants, increase susceptibility to
infection.
34. Rice is a poor source of most of many essential micronutrients,
especially iron (Fe) and zinc (Zn), for human nutrition
(Zimmermann and Hurrell, 2002).
According to the World Health Organization (2010),
approximately two billion people suffer from iron deficiency.
The polished rice contains an average of only 2 mg kg-1 Fe and
12 mg kg-1 Zn (IRRI, 2006), whereas the recommended dietary
intake of Fe and Zn for humans is 10-15 and 12-15 mg per day,
respectively (Welch and Graham, 2004).
35. Rice actually has a lot of iron, but only in the seed coat.
Because unpeeled rice quickly becomes rancid in tropical and
subtropical climates, the seed is removed for storage.
A major cause is the poor absorption of iron from cereal and
legume-based diets high in phytic acid.
Besides having inherently low levels of Zn, wheat grain is also
rich in substances limiting utilization (bioavailability) of Zn in the
human digestive tract, such as polyphenols and phytic acid
(Welch and Graham, 2004).
36. Phytic acid is the major storage compound of phosphorus in grain.
By binding Zn, phytic acid reduces solubility of Zn in food and
restricts its utilization and retention in human body.
Most of the seed-Zn is located in the embryo and aleurone layer,
whereas the endosperm is very low in Zn concentration (Ozturk
et.al., 2006).
According to a Zn-staining study in wheat seed (Fig. 3), Zn
concentrations were found to be around 150 mg kg−1 in the
embryo and aleurone layer and only 15 mg kg−1 in the
endosperm (Ozturk et.al., 2006).
37. Embryo Aleuron Endosperm
Diphenyl thiocarbazone (DTZ) staining a wheat seed. When reacting with
Zn, DTZ forms a red DTZ-complex which indicates localization of Zn
(Ozturk et.al., 2006)
DTZ staining at increasing
Zn concentrations, mg kg-1
39. Over one third of the world's soils are considered Fe deficient.
In order to deal with the limiting amounts of Fe, plants have
evolved several strategies to obtain Fe from the soil.
The Strategy I mechanism includes proton extrusion to
solubilize Fe(III) in the soil, reduction of the solubilized
Fe(III) by a membrane-bound Fe(III) chelate reductase and
subsequent transport of the resulting Fe(II) into the plant root
cell by the Fe(II) transporter IRT1.
40. Strategy II is a chelation-based strategy involving release of
Fe(III)-specific phytosiderophores (PS) and subsequent uptake of
the Fe(III)-phytosiderophore complexes via a specific transport
system.
41. • Several groups have initiated efforts to increase iron by
expressing the ferritin gene from soyabean (Goto et al., 1999;
Drakakaki et al., 2000) and bean (Lucca et al., 2000) in rice
seed.
• Malnutrition of Fe and Zn which may weaken immune function
and impair growth and development of human (Welch, 2002)
afflict more than 50% of the world’s population (Tucker, 2003;
Welch, 2005).
• Zn and Fe deficiencies ranked 5th and 6th among the 10 most
important factors in developing countries.
42. Approaches for increasing the amount of iron
absorbed from rice-based meals
1. Introduced a ferritin gene from Phaseolus vulgaris
into rice grains, increasing their iron content up to two-
fold.
2. To increase iron bioavailability, introduced a
thermotolerant phytase from Aspergillus fumigatus into
the rice endosperm.
3. As cysteine peptides are considered a major
enhancer of iron absorption, overexpressing the
endogenous cysteine-rich metallothionein-like protein.
43. Plant Genes Help to Mobilize and Store Iron
One gene encodes nicotianamine synthase, the enzyme that
produces nicotianamine.
Nicotianamine chelates (metal ion) iron temporarily and facilitates its
transport in the plant.
Nicotianamine synthase is expressed under a constitutive promoter.
The second gene encodes the protein ferritin (consists of 24
subunits), which functions as a storage depot for up to four thousand
iron atoms per protein molecule in both plants and humans.
Iron Biofortification of Rice Targeted Genetic Engineering
Friday, January 22, 2010
By Christof Sautter and Wilhelm Gruissem
• .
44. Since the ferritin gene is under the control of an endosperm-
specific promoter, ferritin comprises a sink for iron in the center of
the endosperm.
The synergistic action of these two genes allows the rice plant to
absorb more iron from the soil, transport it in the plant, and store it
in the rice kernel.
A third gene encoding phytase was also engineered into this rice
line.
Phytase degrades phytate, a compound that stores phosphate
and binds divalent cations like iron and thus inhibits their
absorption in the intestine.
45. The genetically engineered lines expressing nicotianamine
synthase, ferritin, and phytase (NFP-line) contain up to a 6.3-fold
increase of iron in the endosperm of polished kernels as compared
to wild type.
It is significantly more than the lines that contain only single genes,
i.e., nicotianamine synthase (NAS) or ferritin (FER).
Maintenance of Iron Homeostasis
One obstacle to iron biofortification of plants is the toxicity of iron
when it accumulates to higher concentrations in cytoplasm.
46. Plants regulate the uptake and concentration of iron in their cells by
altering nicotianamine concentration through the activity of
-nicotianamine synthase (NAS)
-or a degrading enzyme, nicotianamine amino transferase (NAAT),
in response to an iron-dependant signal.
Constitutive expression of nicotianamine synthase in combination
with ferritin in the endosperm increases iron in sink tissue, but does
not change iron homeostasis in leaves, despite higher levels of
nicotianamine.
Expression of the gene for nicotianamine-degrading NAAT is
stimulated, by higher levels of nicotianamine in leaves of NFP-
plants.
47. Iron biofortification in rice by the introduction of
multiple genes involved in iron nutrition
(Masuda et.al., 2012; Science Reports)
• Goto et.al., 1999 generated transgenic rice plants that
expressed the soybean ferritin gene, SoyferH1, in the
endosperm using the endosperm-specific 1.3-kb GluB1 rice
promoter; the transformants showed higher Fe accumulation
in brown rice seeds.
• Qu et.al., 2005 expressed SoyferH1 under the control of both
the OsGlb1 promoter and 1.3-kb GluB1 promoter to further
increase seed Fe concentration.
• But enhancement of ferritin expression did not produce further
increases in seed Fe content.
48. Therefore, in addition to increased Fe storage in seeds,
enhanced Fe uptake from the soil and enhanced translocation
within the plant body were thought to be required to further
improve Fe biofortification in seeds.
Takahashi et.al., 2003 produced NA-deficient transgenic tobacco
plants that showed young leaves with serious chlorosis, and Fe
and Zn concentrations in the leaves and flowers decreased as a
result of disrupted internal metal transport.
Enhancement of Fe flux into the endosperm occurs by
expression of the Fe(II)-NA transporter gene OsYSL2.
Koike et.al., 2004 identified the rice NA-Fe(II) transporter
gene OsYSL2, which is preferentially expressed in leaf phloem
cells, the vascular bundles of flowers, and developing seeds,
suggesting a role in internal Fe transport.
49. OsYSL2 knockdown mutant plants exhibit a 30% decrease in Fe
concentration in the endosperm.
Simple overexpression of OsYSL2 by the 35S promoter did not
increase Fe concentration in seeds.
In contrast, enhancement of OsYSL2 expression under the control
of the rice sucrose transporter promoter OsSUT1, which drives high
expression in immature seeds during the seed maturation stage.
increased Fe concentration in polished rice seeds by up to
threefold.
50. Introduction of mugineic acid synthase gene was reported as
another approach to increase Fe concentration in seeds.
In graminaceous plants, NA is the precursor of mugineic acid
family phytosiderophores (MAs), which are natural Fe(III) chelators
used in Fe acquisition from the rhizosphere.
Graminaceous plants synthesize and secrete MAs into the
rhizosphere by TOM1 transporter.
They form Fe(III)–MAs complexes and are taken up into the root via
YS1 and YSL transporters.
Rice biosynthesizes 2′-deoxymugineic acid (DMA), which facilitates
Fe uptake and internal transport.
51. Rice lacks IDS3 gene (MA synthase gene) and does not produce
MA.
Fe concentration in polished rice seed increased up to 1.25 to 1.4
times by introduction of barley IDS3 genome fragment.
Each of these approaches could increase Fe concentration in
polished rice seeds.
But a higher Fe concentration in seeds was required to reduce the
human Fe deficiency anemia health problem.
A combination of these transgenic approaches would further
increase the Fe concentration in seeds.
New transgenic rice lines with enhanced Fe accumulation in seeds
using the Soybean ferritin gene under the control of two
endosperm-specific promoters, the OsGlb1 and GluB1.
52. These seeds exhibited enhanced Fe transportation within the plant
body due to over expression of NAS and enhanced Fe translocation
to seeds due to OsYSL2 expression under the control of
the OsSUT1 promoter and OsGlb1 promoter.
Gene insertion, ferritin accumulation in seeds, and higher
expression of OsYSL2 and HvNAS1 were confirmed.
Abundant NA facilitates formation of Fe(II)–NA, which is stable
under higher pH conditions, such as in phloem sap (pH 8.0).
Consequently, Fe(II) transport in the plant body, including the
phloem, is improved by NAS overexpression.
Increasing the NA concentration by enhancing NAS expression may
improve the bioavailable mineral content of rice grains.
53. Fe is well absorbed by the human gastrointestinal tract from
soybean ferritin (Lonnerdal B, 2009).
Increased NA in rice will likely reduce the rates of high-blood
pressure disease (Usuda K. et.al., 2009).
Zn concentration also increased in Fer-NAS-YSL2 lines.
Some reports show that higher NA production increases the Zn
concentration in seeds of rice plants (Masuda H. et.al., 2009).
Endosperm-specific ferritin expression also contributes to the
increased Zn concentration in rice seeds (Vasconcelos M. et.al.,
2003).
55. Seeds of higher plants contain large quantities of storage proteins.
These proteins have been classified on the basis of their solubility
in various solvents.
Albumins (soluble in water)
Globulins (soluble in salt solution)
Prolamins (alcohol soluble)
Glutelins (soluble in acidic or
basic solution)
Wheat, barley, maize, sorghum accumulate major storage
proteins which are low in lysine.
Storage proteins of legumes are insufficient in sulfur-
containing amino acids.
found in dicot plants
found in monocot plants
56. Barley, rice, wheat, sorghum are also low in threonine and maize in
tryptophan.
Food Limiting amino acids
Cereals lysine, threonine, sometimes
tryptophan
Pulses Methionine, tryptophan
Nuts & oilseeds Lysine
Green leafy vegetable
MethionineLeaves & grasses
EAA DEFICIENT IN SOME VEGETARIAN FOODS
57. Three molecular approaches are being used in
altering amino acid sequence
1. Identification of naturally occuring seed storage plant with high
levels of desired amino acids, followed by cloning the
corresponding gene and expressing it at high levels in the
species distinctly differ from the sources of genes.
2. Modification by recombinant DNA technologies so that they
encode proteins similar to wild type proteins but possess
higher levels of desired amino acids.
3. Modification in the pool size of the desired amino acids for the
synthesis of seed storage proteins by an alternative metabolic
pathway.
57
58. Examples of expression of recombinant storage proteins with
desirable amino acid profiles:
Expression of pea (Pisum sativum) legumin, which has a high
lysine content, in rice and wheat grains (Stoger et.al., 2001).
The expression of sunflower seed albumin, which is rich in
methionine, in the laboratory model lupin (Molvig et.al., 1997).
59. In India, a genetically modified potato has been developed by a
coalition of charities, scientists, government institutes and industry
as part of a 15-year plan to combat malnutrition amongst India's
poorest children.
The 'protato', contains a gene AmA1 from the South American
amaranth plant, resulting in an increased protein content of 2.5 per
cent.
AmA1 gene from the Prince’s feather (Amaranthus
hypochondriacus), which encodes seed albumin, was expressed in
potato and was shown to double the protein content and increase the
levels of several essential amino acids (Chakraborty et.al., 2000).
The protato has high levels of essential amino acids, lysine and
methionine.
Protein-rich potato
• .
60. GM maize with increased lysine (LY038) was developed by
inserting a cordapA gene from a common soil
bacteria Corynobacterium glutamicum.
Enhanced production and accumulation of free lysine (Lys) in
the GM corn kernel made body weight gain, feed conversion and
carcass yields of experimental poultry and swine comparable
with animals fed with Lys supplemented diets, and higher than
those fed with conventional maize diets (Lucas DM et.al., 2007).
Lys-enriched maize with the gene sourced from potato, was also
found to be safe as conventional maize (He XY et.al., 2009).
LY038 has been commercialized and incorporated in feed meals
since 2006.
61. In all higher plants, lysine, threonine and methionine are
synthesized from aspartic acid via a pathway that is highly
branched and under complex feedback control.
62. Two key enzymes are aspartate kinase (AK), which functions
early in the pathway and is inhibited by both lysine and
threonine.
Dihydrodipicolinate synthase (DHPS), which functions in the
lysine-specific branch and is inhibited by lysine alone.
Feedback- insensitive versions of the bacterial enzymes have
been expressed in plants with promising results:
the free lysine content of Arabidopsis seeds was increased either
by expressing a bacterial, feedback-insensitive DHPS
transgene
or by knocking out the lysine catabolism pathway,
resulting in 12-fold or fivefold gains in lysine, respectively.
63. Where both the transgene and knockout were combined in the
same Arabidopsis line, increases of 80-fold overwild-type
levelswere achieved (Zhu X and Galili G, 2003).
Protein-enriched soybean event M703 was found to contain more
digestible amino acids lysine, methionine, threonine, and valine,
and had a higher level of metabolizable energy (Edwards HM et.al.,
2000).
A maize γ-zein gene encoding a sulphur amino acid rich protein
was used to transform alfalfa and trefoil (Lotus corniculatus) under
CaMV 35S promoter and RUBISCO small subunit promoter.
Expression level was rather low to the extent of 0.05% of alcohol
soluble protein.
64. To increase methionine level, a new methionine-rich zein,
normally expressed at low levels was expressed at a high level
using the 27 kDa zein promoter.
This protein called the high sulphur zein (HS 7) was 21 kDa and
contained 37% Met.
Biotechnology offers great potential for the production of novel
design crops, which are the sole solution to safeguard the supply of
sufficient quantities of safe & healthy food tomorrow.
The β–carotene synthesis pathway involves multiple enzymes.This important vitamin A precursor cannot be synthesized in rice because it lacks four of the key enzymes.Therefore, the precursor is not made, and the plant contains white kernels.
In a major feat of genetic engineering, scientists inserted a complete functioning -carotene biosynthetic pathway into the rice plant. They did this by inserting genes from daffodil to produce functioniong versions of the first and last enzymes of the pathway. In addition, a single bacterial gene that provides the same function as the second and third enzymes of the pathway, was also introduced. With a functioning pathway, the transgenic rice is able to produce the vitamin A precursor β-carotene. It is this product that gives "Golden Rice" its characteristic yellow color.