'Genomics' is nothing but the study of entire genetic compliment of an organism. Plant genomics is study of plant genome. This is my topic of M.Sc. course 'Plant biotechnology'.
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.
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
A plant genome project aims to discover all genes and their function in a particular plant species.
The main objective of genomic research in any species is to sequence the whole genome and functions of all the different coding and non-coding sequences.
These techniques helped in preparation of molecular maps of many plant genomes.
Plant genome projects initially focused on a few model organisms that are characterized by small genomes or their amenability to genetic studies
Since sequencing technologies have moved on, sequencing cost have dropped and bioinformatics tools advanced, the genomes of many plant species including the enormous genome of bread wheat have been assembled
Genome sequencing projects have been carried out on all three plant genomes: the nuclear, chloroplast and mitochondrial genomes
This opened venues for advanced molecular breeding and manipulation of plant species, but also have accelerated phylogenetics studies amongst species
Several excellent curated plant genome databases, besides the general nucleotide data base archives, allow public access of plant genomes
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
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.
'Genomics' is nothing but the study of entire genetic compliment of an organism. Plant genomics is study of plant genome. This is my topic of M.Sc. course 'Plant biotechnology'.
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.
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
A plant genome project aims to discover all genes and their function in a particular plant species.
The main objective of genomic research in any species is to sequence the whole genome and functions of all the different coding and non-coding sequences.
These techniques helped in preparation of molecular maps of many plant genomes.
Plant genome projects initially focused on a few model organisms that are characterized by small genomes or their amenability to genetic studies
Since sequencing technologies have moved on, sequencing cost have dropped and bioinformatics tools advanced, the genomes of many plant species including the enormous genome of bread wheat have been assembled
Genome sequencing projects have been carried out on all three plant genomes: the nuclear, chloroplast and mitochondrial genomes
This opened venues for advanced molecular breeding and manipulation of plant species, but also have accelerated phylogenetics studies amongst species
Several excellent curated plant genome databases, besides the general nucleotide data base archives, allow public access of plant genomes
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
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.
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
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.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
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.
Comparative genomics in eukaryotes, organellesKAUSHAL SAHU
WHAT IS COMPARATIVE GENOMICS?
HISTORY
SOME RELATED TERMS
MINIMAL EUKARYOTIC GENOMES
COMPARISON OF THE MAJOR SEQUENCED GENOMES
EUKARYOTIC GENOMES
SACCHAROMYCES CEREVISIAE GENOME
INSECT GENOME
DROSOPHILA MELANOGASTER (FRUIT FLY) GENOME
COMPARATIVE ANALYSIS OF THE HUMAN AND MOUSE GENOME
COMPARATIVE GENOMICS OF ORGANELLES
COMPARATIVE GENOMICS TOOLS
CONCLUSION
REFERENCES
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
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.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
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.
Comparative genomics in eukaryotes, organellesKAUSHAL SAHU
WHAT IS COMPARATIVE GENOMICS?
HISTORY
SOME RELATED TERMS
MINIMAL EUKARYOTIC GENOMES
COMPARISON OF THE MAJOR SEQUENCED GENOMES
EUKARYOTIC GENOMES
SACCHAROMYCES CEREVISIAE GENOME
INSECT GENOME
DROSOPHILA MELANOGASTER (FRUIT FLY) GENOME
COMPARATIVE ANALYSIS OF THE HUMAN AND MOUSE GENOME
COMPARATIVE GENOMICS OF ORGANELLES
COMPARATIVE GENOMICS TOOLS
CONCLUSION
REFERENCES
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you could send your comments..
And I'm willing to help you in similar works.I'm in final year of my degree(.BSc Biotechnology)..
pubudu_gokarella@yahoo.com
genome structure and repetitive sequence.pdfNetHelix
Welcome to our channel, where science meets discovery! In today's enlightening video, we unravel the mysteries of life at its most fundamental level - the chromosomes.
Join us on an exhilarating journey deep within the human cell as we explore the intricate architecture and organization of these tiny yet immensely powerful structures.
Don't forget to subscribe to the channel and hit the notification bell to stay updated with all the latest and exciting content. Thank you for your continuous support and for watching us.
Introduction
History
Tumor suppressor gene- pRB
- RB gene
- Role of RB in regulation of cell cycle
- Tumor associated with RB gene mutation
Tumor suppressor gene- p53
- What is p53 gene?
- Function of p53 gene
- How it regulates cell cycle
- What happen if p53 gene inactivated
- Cancer associated with p53 mutation
- Conclusion
- References
Introduction
Definition
History
Two hit hypothesis
Functions
Mutation in tumor suppressor genes
What is mutation
Inherited mutation of TSGs
Acquired mutation of TSGs
What is Oncogenes?
TSGs and Oncogenes : Brakes and accelerators
Stop and go signal
Examples of TSGs:
RB-The retinoblastoma gene
P53 protein
TSGs &cell suicide
Conclusion
References
Introduction
Protein synthesis
Synthesis of secretory proteins on membrane-bound ribosomes
Processing of newly synthesized proteins in the ER
Synthesis of integral membrane protein on membrane bound ribosomes
Maintenance of membrane asymmetry
Conclusion
Reference
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
Introduction
Definition
History
central dogma
Major components
mRNA,tRNA,rRNA
Energy source
Amino acids
Protien factor
Enzymes
Inorganic ions
Step involves in translation:
Aminoacylation of tRNA
Initiation
Elongation
termination
Importance of translation
Conclusion
Reference
Introduction
Protein modifications
Folding
Chaperon mediated
Enzymatic
Cleavage
Addition of functional groups
Chemical groups
Hydrophobic groups
Proteolysis
Conclusion
Reference
INTRODUCTION
HISTORY
WHAT IS TRANSCRIPTION
PROKARYOTIC TRANSCRIPTION
STEPS OF TRANSCRIPTION
HOW TRANSCRIPTION OCCURS
PROCESS OF TRANSCRIPTION
Initiation
Elongation
Termination
CONCLUSION
REFRENCES
Enzyme Kinetics and thermodynamic analysisKAUSHAL SAHU
Introduction
Kinetics and thermodynamicSG
Thermodynamic in enzymatic reactions
balanced equations in chemical reactions
changes in free energy determine the direction & equilibrium state of chemical reactions
the rates of reactions
Factors effecting enzymatic activity
(i) Enzyme concentration.
(ii) Substrate concentration.
(iii)Temperature
(iv) pH.
(v) Activators.
(vi)Inhibitors
Michaelis-menten equation
CONCLUSIONS
REFERENECES
Recepter mediated endocytosis by kk ashuKAUSHAL SAHU
INTRODUCTION
DEFINITION OF RECEPTOR MEDIATED ENDOCYTOSIS
WHAT TYPE OF LIGANDS ENTER BY RME?
FORMATION OF CLATHRIN-COATED VESICLES
TRISKELIONS
ROLE OF DYNAMIN IN THE FORMATION OF CLATHRIN-COATED VESICLES
ROLE OF PHOSPHOLIPIDS IN THE FORMATION OF COATED VESICLES
ENDOCYTIC PATHWAY
LDLs AND CHOLESTROL METABOLISM
CONCLUSION
REFERENCES
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Prokaryotic translation machinery by kk KAUSHAL SAHU
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
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.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
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.
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.
1. PLANT GENOMICS
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )
2. CONTENTS:
Introduction
History
First model organism(Arabidopsis thaliana)
Studying plant genome
Plant nuclear genome composition
Organization of plant genome
Transposable elements
Chloroplast genome & its evolution
Mapping plant genomes
Plant genome project
Application
Conclusion
References
3. Introduction
Genomics - the study of genomes.
Genome -The word ‘’genome’’describes the total
repertoire of DNA in a particular organelle.
Plant genomes dramatically vary in size and in
function.
Plant chloroplasts and mitochondria maintain plant
genomes, and plant mitochondrial genomes are large,
variable and enormously interesting.
Plant nuclear genomes have been sculpted by
interspecific hybridization ,polyploidy, transposition,
retro-transposition and translocation events.
4. History :
Formal research into the function of the plant
genome started with mendel in 1866 .
Arabidopsis thaliana (a dicot) was the first plant
chosen for genome sequencing, Rice was the
second genome sequenced and was the first
monocot.
A small number of plant genomes have been
studied in great detail in the 1990s and early in the
twenty-first century and the DNA of their genomes
has been sequenced.
5. First eukaryotic model
organism(Arabidopsis thaliana)
One of the first eukaryotic organisms that will be
completely sequenced is the small mustard species
Arabidopsis thaliana.
During the past decade, Arabidopsis has emerged
as one of the most widely used model organisms for
studying the biology of higher plants.
It was chosen for sequencing because it has a highly
compact genome of about 130 Mb with little
interspersed repetitive DNA.
6. Fig.: Functional classification of predicted genes in
a 1.9-Mb region of the Arabidopsis genome.
7. Studying Plant genome:
Plant genomes are more complex than other eukaryotic
genomes, and analysis reveals many evolutionary flips and
turns of the DNA sequences over time.
Plant nuclear genome range in size from less than
100million base pairs to more than 100 billion base pairs.
Plants show widely different chromosome numbers and
varied ploidy levels . Overall, the size of plant genomes
(both number of chromosomes and total nucleotide base-
pairs) exhibits the greatest variation of any kingdom in the
biological world. For example, tulips contain over 170 times
as much DNA as the small weed Arabidopsis thaliana.
8. The DNA of plants, like animals, can also contain
regions of sequence repeats, sequence inversions, or
transposable element insertions, which further modify
their genetic content.Traditionally, variation in
chromosome inversions and ploidy has been used to
build up a picture of how plant species have evolved .
Increasingly,researchers are turning to studying the
organization of plant DNA sequences to obtain
important information about the evolutionary history of
a plant species.
9. FIGURE : Chromosome numbers possible in plant
genomes.
10. Nuclear Genomes and their Size
The nuclear genome of rice consists of 450 million base
pairs (Mbp) of DNA divided among the 12 chromosome
pairs, and includes the genes that encode some 38 000
proteins.
Along with their controlling sequences, these genes
represent less than 10% of the total amount of DNA, and
about half of all the DNA consists of repetitive motifs that
are present thousands of times in the genome.
Another fully sequenced plant genome,Arabidopsis
(Arabidopsis thaliana) has a total of 157Mbp with about
31 000 genes on five chromosome pairs.
11. It is currently anticipated that the complete genome
sequence of Arabidopsis will be available by the end of the
year 2000.
Because Arabidopsis is only distantly related to the cereal
crops that provide the bulk of the world’s food supply, the
genome of rice will also be sequenced during the next
decade .
Rice was chosen because, in addition to its importance as a
food source for about one-quarter of the human population,
it has one of the most compact genomes among the cereals.
It contains about 3.5 times as much DNA as Arabidopsis but
only about 20% as much DNA as maize and about 3% as
much DNA as wheat .
12. All higher plants, at the diploid level, require
approximately the same number of genes and
regulatory DNA sequences for physiological processes
like seed germination,growth, flowering and
reproduction.
However, nuclear genome sizes, measured by the
number of base pairs of DNA, of different plant species
vary enormously between species, although each
species has a characteristic and relatively constant
genome size.
The amount of nuclear DNA can be given as an
absolute weight of the DNA (in pg, picograms) or
converted into the number of base pairs represented by
that weight.
13.
14. Plant Nuclear Genome Composition
The plant nuclear genome consists of DNA divided
among the chromosomes within the cell nucleus.
Plant genomes contain coding and regulatory
sequences for the genes and repetitive DNA.
Genomes are evolutionarily dynamic and analysis
provides insights into the evolution of genes,
sequence families and genomes, and supports
studies of species phylogeny and relationships.
15. The plant nuclear genome consists of
deoxyribonucleic acid (DNA) and is contained
within the nucleus, an organelle encased by a
double membrane in each cell.
During cell division, mitosis, the genome
condenses into a characteristic number of
metaphase chromosomes, the nuclear membranes
break down, and the chromosomes divide, moving
into the two daughter cells before the nuclei reform.
16. Organization of Plant Genomes:-
Most seed plants contain quantities of DNA that
greatly exceed their needs for coding and
regulatory function. Hence, for plants, a very small
percentage of the genome may actually encode
genes involved in the production of protein.
This portion of the genome which encodes most of
the transcribed genes is often referred to as “low-
copy number DNA,” because the DNA sequences
comprising these genes are present in single or
small numbers of copies.
17. “Medium-copy-number DNA” is composed largely
of DNA sequences that encode ribosomal RNA
(rRNA), a key element of the cellular machinery that
translates transcribed messenger RNA (mRNA) into
protein.
In plant genomes, rRNA genes may be repeated
several hundred to several thousand times.
Plant cells may also contain excess DNA in their
genomes in the form of highly repetitive sequences,
or “high-copy-number DNA.” At present, the
function of this high-copy-number DNA in plant
genomes is unknown.
18. Sequence Replication and
Inversion
High-copy-number DNA sequences in the plant
genome may be short, such as the nucleotide sequence
“GAA,” or much longer, involving up to several hundred
nucleotides.
Moreover, the number of copies of an individual high
copy repetitive DNA sequence can total from 10,000 to
100,000.There are several possibilities for how high-
copy repetitive DNA sequences may be organized
within a plant genome.
Several copies of a single repetitive DNA sequence may
be present together in the same orientation, in a
pattern called “simple tandem array.”
19. Alternatively, repetitive DNA sequences can be dispersed among
single-copy DNA in the same orientation (“repeat/single-copy
interspersion”) or the opposite orientation (“inverted repeats”).
In addition, groups of repetitive DNA sequences can also occur
together in plant genomes in a variety of possible arrangements,
such as a“compound tandem array” or a “repeat/repeat
interspersion.”
The presence of repetitive DNA can vastly increase the size of a
plant genome, making it difficult to find and characterize individual
single-copy genes.
A variety of mechanisms can account for the presence of highly
repetitive DNA sequences in plant genomes.
20. Transposable Elements:
Transposable elements, are special sequences of DNA with
the ability to move from place to place in the genome.
They can excise from one site at unpredictable times and
reinsert in another site. For this reason, transposable
elements have been called “jumping genes.
Transposable elements often insert into coding regions or
regulatory regions of a gene and so affect expression of that
gene, resulting in a mutation that may or may not be
detectable.
Barbara McClintock won the Nobel Prize in 1983 for her
work describing transposable elements in corn.
21.
FIGURE : Organization of repeated DNA sequences and the
mechanism of transposable elements in altering gene function.
22. Chloroplast Genome and Its
Evolution
The chloroplast is a plant organelle that functions in
photosynthesis,and it can independently replicate in the
plant cell.
Plant chloroplasts have their own specific DNA, which is
separate from that present in the nucleus.
This DNA is maternally inherited and encodes unique
chloroplast proteins.
Many of the proteins encoded by chloroplast DNA are
involved in photosynthesis.
23. Chloroplast DNA is present as circular loops of
double-stranded DNA similar to prokaryotic
chromosomal DNA.
Moreover, chloroplast DNA contains genes for
ribosomes that are very similar to those present in
prokaryotes.The DNA in chloroplasts of all land
plants has about the same number of genes (~100),
and they are present in about the same order .
25. Mapping plant genomes:
RFLP and AFLP asTools to Map Genomes and Detect
Polymorphisms
Genome mapping is a widely-Aplicable approach to
scanning the genetic information of an organism for genes
that are responsible for a specific trait.
Higher plants are thought to have 25,000 or more genes,the
vast majority of which remain of unknown function.
A particular strenghth of genome mapping.is that it
facilitates isolation of genes based simply on measurement
of their effects(s)on phenotype requiring no a priori
knowledge of the biochemical function performed by a
gene.
26. Much more of the genome can be mapped using RFLPs
(restriction fragment length polymorphisms) which need
not have a macroscopic phenotype.
This approach, involves analysis of the RFLP map, or the
pattern of DNA fragments, produced when DNA is treated
with restriction enzymes that cleave at specific sites.
RFLP mapping can identify important regions of the
genome at a glance, while sequence data require
sophisticated computer- based searching and matching
systems.
A comparison of the RFLP maps of parents and progeny
can give an indication of the heritability of gene traits and of
heritable loci that are characteristic of traits.
27. Another tool that utilizes sequence variability is AFLPs,
or amplified fragment length polymorphisms.
Hybridizing DNA primers with genomic DNA
fragments that have been cut with restriction enzymes,
usually EcoRI and MseI, and then subsequently
amplified using the polymerase chain reaction (PCR)
generates AFLP maps.
The resulting PCR products, which represent each piece
of DNA cut by a restriction enzyme, are separated by
size via gel electrophoresis.
The band sizes on an AFLP gel tend to show more
polymorphisms than those found with RFLP mapping
because the entire genome is visible on the gel .
28. Applications:
Genomics research will lead to new and innovative ways
to
achieve such trait improvement. Clearly,genomics can
help in issues related to food safety, food quality,and
food diversity.
Genomics provides objectivity in breeding as never
before possible; it allows hypothesis testing of
quantitative genetics applications in plant
improvement.
It is useful to increase crop productivity, improve crop
quality, and maintain the environment.
29. Conclusion:
Genomic organization is much more varied in plants
than in animals.The completely sequenced
Arabidopsis genome will have far-reaching uses in
agricultural breeding and evolutionary analysis.
Plant genome research is more than biology; it is
also about producing food for our planet.
30. References
Plant genomics and proteomics-Christopher
A.Cullis, A. Jhon & Sons,Inc.Publication (pdf).
Biotechnology –vol-VII plant genome mapping
strategies & application – Andrew H.Peterson(pdf).