This document discusses functional genomics and its approaches. It defines functional genomics as the worldwide experimental approach to access the function of genes by using information from structural genomics. The key functional genomics approaches discussed are transcriptomics, proteomics, metabolomics, interactomics, epigenetics, and nutrigenomics. Modern techniques discussed include expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and microarray analysis.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
Introduction
History
Genetic mapping
DNA Markers
Physical mapping
Importance
Drawback
Conclusion
References
uses genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees).
The study of the complete set of RNAs (transcriptome) encoded by the genome of a specific cell or organism at a specific time or under a specific set of conditions is called Transcriptomics.
Transcriptomics aims:
I. To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.
II. To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications.
III. To quantify the changing expression levels of each transcript during development and under different conditions.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. [Source: https://opentextbc.ca/biology/chapter/10-3-genomics-and-proteomics/]
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
The study of the complete set of RNAs (transcriptome) encoded by the genome of a specific cell or organism at a specific time or under a specific set of conditions is called Transcriptomics.
Transcriptomics aims:
I. To catalogue all species of transcripts, including mRNAs, noncoding RNAs and small RNAs.
II. To determine the transcriptional structure of genes, in terms of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications.
III. To quantify the changing expression levels of each transcript during development and under different conditions.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
A physical map of a chromosome or a genome that shows the physical locations of genes and other DNA sequences of interest. Physical maps are used to help scientists identify and isolate genes by positional cloning.
According to the ICSM (Intergovernmental Committee on Surveying and Mapping), there are five different types of maps: General Reference, Topographical, Thematic, Navigation Charts and Cadastral Maps and Plans.
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. [Source: https://opentextbc.ca/biology/chapter/10-3-genomics-and-proteomics/]
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
The analysis of global gene expression and transcription factor regulation, global approaches to alternative splicing and its regulation, long noncoding RNAs, gene expression models of signalling pathways, from gene expression to disease phenotypes, introduction to isoform sequencing, systematic and integrative analysis of gene expression to identify feature genes underlying human diseases.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the American Chestnut & Chinese Chestnut Genomics research community.
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
Introduction to Apollo: A webinar for the i5K Research CommunityMonica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project Species.
1.introduction to genetic engineering and restriction enzymesGetachew Birhanu
An introduction to Genetic engineering
A short background and history of Genetic Engineering
Classification of DNA manipulating Enzymes, nomenclature
Restriction recognition sequences, the anatomy of a gene and the flow of genetic information
More emphasis is given for the essential DNA Manipulating Enzymes
Finally Restriction mapping (analysis)
Apollo : A workshop for the Manakin Research Coordination NetworkMonica Munoz-Torres
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
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.
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.
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.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
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.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
2. Genomics is the field of genetics that attempt to understand the content,
organisation, function and evolution of genetic information contained in whole
genome.
GENOMICS
Types of genomics:
•Structural genomics: Structural Genomics is a worldwide effort aimed at determining the
three-dimensional structures of gene products in an efficient and high-throughput mode.
•Comparative genomics : Comparative genomics is a field of biological research in which
the genomic features of different organisms are compared. The genomic features may
include the DNA sequence, genes, gene order, regulatory sequences, and
other genomic structural landmarks
•Functional genomics : Functional genomics is the worldwide experimental
approach to access the function of gene by making use of information and reagent provided
by structural genomics. - Hieter & Boguski 1997
6. Functional Genomics Approaches
1. Transcriptomics: Transcriptomics studies measure gene
expression at the transcript or RNA level.
2. Proteomics: Proteomics approaches focus on which proteins
are expressed in a biological system but may also include
studies of protein structure.
3. Metabolomics: Metabolomics is the study of all metabolites
in a biological system
4. Interactomics: Together, transcriptomics, proteomics,
metabolomics describe the transcripts, proteins and
metabolites of a biological system and expected to provide a
complete model of the biological systems being studied.
7. Interactomics, is of specific relevance to
agriculture systems, particularly in understanding
disease. Interactomics is the study of the molecular
interactions and encompasses host– pathogen
interactions
5.Epigenetics: Epigenetics studies non-heritable
changes in the genome (e.g., DNA methylation and
histone modification) that affects observed phenotypes.
6. Nutrigenomics:. Nutrigenomics (or ‘nutritional
genomics’) focuses on understanding how diet affects
gene expression.
Conti…
8. •Transcription profiling
This is one of the most popular study types, also known as
'expression profiling'. It involves the quantification of gene
expression of many genes in cells or tissue samples at the
transcription (RNA) level.
The quantification can be done by collecting biological
samples and extracting RNA (in most cases, total RNA) following
a treatment or at fixed time-points in a time-series, thereby
creating 'snap-shots' of expression patterns.
Branches of Functional Genomics
10. Genotyping
Genotyping studies are those which identify differences
in the DNA sequence (i.e genotype) of a sample. with the aim of
identifying differences in the genotype which may explain the
difference in phenotype.
Genotyping studies can be designed to identify DNA
sequence differences at three levels:
•Single nucleotide polymorphisms (SNPs, pronounced ‘snips’):
SNP analysis focuses on differences in the DNA sequence at the
single nucleotide level.
Example: SNP-profiling of plasma DNA in breast cancer patients
11. •Copy number variations (CNVs): CNVs refer to an increase or
decrease in the number of copies of a segment of DNA (e.g. a
gene, or a locus-specific DNA repeat element). Each 'copy' can be
as short as 50 bases or up to 100 kilo bases.
Example: A genome-wide copy number variant study of suicidal
behavior
•Structural variations: they are an order of magnitude larger
than CNVs and often cover megabases of DNA.
Example: Transcription profiling by high throughput sequencing
of different maize lines to discover and characterise 'presence-
absence variation' in the maize genome
Conti…
12. Epigenetic profiling
Epigenetics is the study of how biochemical
modifications or physical interaction of DNA/chromatin
affect gene regulation in a cell.
At the DNA level, methylation of CpG
dinucleotides (often located near gene promoters) can be
detected by first converting unmethylated cytosines
into uracil using bisulfite, which allows methylated and
unmethylated cytosines to be distinguished.
.
Example: Quantitative sequencing of 5-methylcytosine
and 5-hydroxymethylcytosine
13. DNA/RNA-protein interactions
Transcription factors, ribosomes and other
DNA/RNA-binding proteins can bind to nucleic acid
sequences and influence the transcription
and translation of genes. The immunoprecipitation
technique has also been applied to study protein
binding sites on RNA.
14. Meta-analysis
Meta-analysis is a branch of functional genomics in
which data from pre-existing experiments is combined to
create statistically more powerful models of a biological
process. This type of analyses has become popular as it
allows the identification of subtle events that could not be
detected in smaller studies. Functional genomics databases
such as ArrayExpress and Expression Atlas play an
important role in these studies as reliable, well annotated
sources of functional genomics data.
Example: Genome-wide analysis of over 106,000
individuals identifies 9 neuroticism-associated loci
15. Techniques in Functional Genome Analysis
1.Classical techniques and tools
• Inserstional mutagenesis : Insertional mutagenesis is mutagenesis of
DNA by the insertion of one or more bases.
e.g. Transposons and T- DNA tagging
• Sequence based mutagenesis : It is a molecular biology method that is
used to make specific and intentional changes to the DNA sequence of a
gene.
e.g. Physical and chemical mutagenesis
•Tarrget gene mutagenesis: Homologous recombination can be used to
produce specific mutation in an organism. Vector containing DNA sequence
similar to the gene to be modified is introduced to the cell, and by a process
of recombination replaces the target gene in the chromosome.
e.g. RNAi, Sense and antisense expression
16. 2. Mordern techniques and tools
a. sequence based approaches
EST
SAGE
b. microarray based approaches
17. Expressed sequence tags
•ESTs are short sequences of cDNA typically 200-400 nucleotides in length.
•Obtained from either 5’ end or 3’ end of cDNA inserts of cDNA library.
DRAWBACKS OF USING E.S.T
• Automatically generated without
verification thus contain high error rates.
• There is often contamination by vector
sequence , introns, ribosomal RNA,
mitochondrial RNA.
• ESTs represent only partial sequences
of genes.
ADVANTAGES OF E.S.T
• Provide a rough estimate of genes that
are actively expressed in a genome under
a particular physiological condition.
• Help in discovering new genes, due to
random sequencing of cDNA clones.
• EST libraries can be easily generated
18. EST INDEX CONSTRUCTION
“A collection of nonredundant and annotated EST sequence is known as gene
index construction
STEPS INVOLVED
• Remove vector contaminants
• masks repeats using Vecscreen
• Clustering (associates EST sequences with unique
genes)
• Derive consensus sequences results in longer contigs
• Coding region is defined by excluding introns and 3’-
untranslated sequences.
• coding sequence translated into protein sequence
• Alignment of these complied ESTs with genomic
sequence
19.
20.
21. Microarraybasedapproaches
A microarray is a pattern of ssDNA probes which
areimmobilized on a surface called a chip or a slide.
• Microarrays use hybridization to detect a specificDNA
or RNA in a sample.
• DNA microarray uses a million different probes, fixed
on a solid surface.
• Microarray technology evolved from Southern
blotting.
• To analyze the expression of thousands ofgenes in
single reaction, very quickly and in anefficient manner.
Metabolomics: Metabolomics is the study of all metabolites in a biological system and while these are typically not coded for in the genome, they are produced during cell, tissue or organism metabolism
The quantification can be done by collecting biological samples and extracting RNA (in most cases, total RNA) following a treatment or at fixed time-points in a time-series, thereby creating 'snap-shots' of expression patterns.
For common reference genomes with well-annotated transcripts and genes (e.g. the human genome), a researcher can choose to focus on quantifying transcription of all or a subset of transcripts, genes, coding exons, non-coding RNA, and so forth.
The genomic DNA samples are often obtained from two contrasting groups of samples, e.g. drought-resistant rice cultivars vs. drought-sensitive counterparts,
One common extension of genotyping studies in humans are genome-wide association studies (GWAS). Samples from cases (e.g. rheumatoid arthritis patients) and controls (e.g. healthy individuals) are genotyped across specific sites in the genome, followed by statistical analysis to find SNPs which are significantly more prevalent in one group (e.g. the disease cases). Such SNPs may then suggest an association between the SNPs and disease susceptibility.
At the chromatin level, modifications of the tails of histone proteins (e.g. methylation, acetylation) can be mapped by 'immunoprecipitation', where chromatin and proteins are chemically cross-linked reversibly. The genomic DNA associated with the modification/protein of interest is then 'pulled-down' (precipitated) with specific antibodies raised against the modification/protein. After precipitation, the cross-linking is reversed to release the genomic DNA for further analysis
Insertional mutations can occur naturally, mediated by virus or transposon, or can be artificially created for research purposes in the lab.
Target gene mutagenesis This method can be used to introduce a mutation or knock out a gene, for example as used in the production of knockout mice
