1. The document outlines Simon Renny-Byfield's presentation on whole genome duplication and plant genome diversity. It discusses three main topics: the diversification of polyploid genomes, the evolution of duplicated genes following ancient whole genome duplications, and how polyploid genomes become more diploid-like over time through biased fractionation.
2. Polyploid genomes are highly dynamic and vary over time, with different sub-genomes sometimes behaving differently. Duplicated genes also diverge in their expression patterns and functions following ancient whole genome duplications. Most genes are lost in a biased manner after whole genome duplication, contributing to diploidization of polyploid genomes.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
PacBio SMRT - THIRD GENERATION SEQUENCING TECHNIQUEMuunda Mudenda
Nucleic acids sequencing is a very powerful molecular biology and biotechnology technique that gives way to discovery, invention, and solutions. This academic document discusses Single-Molecule Real-Time (SMRT) sequencing platform by Pacific Biosciences (PacBio). The doeucment does not claim to exhaust the subject but you will surely get all the needed highlights to understand this technology better. If you would like an in-depth discussion, do not hesitate to write me an email. Enjoy the read.
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
PacBio SMRT - THIRD GENERATION SEQUENCING TECHNIQUEMuunda Mudenda
Nucleic acids sequencing is a very powerful molecular biology and biotechnology technique that gives way to discovery, invention, and solutions. This academic document discusses Single-Molecule Real-Time (SMRT) sequencing platform by Pacific Biosciences (PacBio). The doeucment does not claim to exhaust the subject but you will surely get all the needed highlights to understand this technology better. If you would like an in-depth discussion, do not hesitate to write me an email. Enjoy the read.
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
The MEGA software is one of the most widely used software tools in molecular taxonomy and bioinformatics. This module describes how MEGA can be employed in a classroom setting to teach the fundamentals of molecular taxonomy.
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.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Gene mapping | Genetic map | Physical Map | DNA Data Analysis (upgraded)NARC, Islamabad
Genes are useful markers but not ideal.
Mapped feature that are not genes are called DNA markers.
DNA markers must have at least two alleles to be useful.
DNA sequence features that satisfy this requirement are-
– Restriction Fragment Length Polymorphism (RFLP)
Southern hybridization
PCR
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)
Mapping- determining the location of elements with in a genome, with respect to identifiable land marks.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.
In simple mapping of genes to specific locations on chromosomes.
Two types
Genetic map
Physical Map
They are useful in predicting results of dihybrid and trihybrid crosses.
It allows geneticists to understand the overall complexity and genetic organization of a particular species.
Identify genes responsible for diseases.
Identify genes responsible for traits.
genetic maps are useful from an evolutionary point of view.
Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.
this presentation gives information about cloning technique such as TOPO Cloning, SLIC and, Golden Gate Cloning.
این ارایه در مورد تکنیک های کلون کردن می باشد
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
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
The MEGA software is one of the most widely used software tools in molecular taxonomy and bioinformatics. This module describes how MEGA can be employed in a classroom setting to teach the fundamentals of molecular taxonomy.
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.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Gene mapping | Genetic map | Physical Map | DNA Data Analysis (upgraded)NARC, Islamabad
Genes are useful markers but not ideal.
Mapped feature that are not genes are called DNA markers.
DNA markers must have at least two alleles to be useful.
DNA sequence features that satisfy this requirement are-
– Restriction Fragment Length Polymorphism (RFLP)
Southern hybridization
PCR
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)
Mapping- determining the location of elements with in a genome, with respect to identifiable land marks.
Gene mapping describes the methods used to identify the locus of a gene and the distances between genes.
In simple mapping of genes to specific locations on chromosomes.
Two types
Genetic map
Physical Map
They are useful in predicting results of dihybrid and trihybrid crosses.
It allows geneticists to understand the overall complexity and genetic organization of a particular species.
Identify genes responsible for diseases.
Identify genes responsible for traits.
genetic maps are useful from an evolutionary point of view.
Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.
this presentation gives information about cloning technique such as TOPO Cloning, SLIC and, Golden Gate Cloning.
این ارایه در مورد تکنیک های کلون کردن می باشد
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
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
The number of sequenced genes having unknown function continues to climb with the continuing decrease in the cost of genome sequencing. In Reverse Genetics (RG), functions of known genes are investigated with targeted modulation of gene activity, and hypothesis regarding gene function directly tested in vivo. Several RG approaches like insertional mutagenesis, fast neutron mutagenesis, TILLING and RNA interference have led to the identification of mutations in candidate genes and subsequent phenotypic analysis of these mutants.
Okabe et al. (2011) employed TILLING technique to screen six ethylene receptor genes in tomato (SlETR1–SlETR6) and two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) with reduced ethylene response were identified. Using fast neutron mutagenesis, Li et al. (2001) obtained arabidopsis deletion mutants for bZIP transcription factor viz. AHBP 1b and OBF 5, a key regulator for systemic acquired resistance but their role were compensated by other regulatory factors in mutants. Terada et al. (2007) successfully blocked the expression of the Adh 2 gene through homologous recombination followed by transgenesis in rice however phenotype could not be determined since no differences were observed between wild and transgenic plants. RNA interference (RNAi) works as sequence-specific gene regulation and has been used in determination of function of many genes. Saurabh et al. (2014) reviewed the impact of RNAi in crop improvement and found its application in improvement of nutritional aspects, biotic and abiotic stresses, morphol¬ogy, crafting male sterility, enhanced secondary metabolite synthesis.
In addition, new advances in technology and reduction in sequencing cost may soon make it practical to use whole genome sequencing or gene targeting like ZFN technology and TAL effectors technology on a routine basis to identify or generate mutations in specific genes. Scholze and Boch (2011) mentioned that TAL effectors technology is more specific and predictable than ZFN. RG techniques have their own advantages and disadvantages depending on the species being targeted and the questions being addressed. Finally, with the continuous development of new technologies, the most efficient RG technique in the future may involve high throughput direct sequencing of part or complete genomes of individual plants followed by efficient novel tools to determine the function for utilization in crop improvement.
DNA Fingerprinting for Taxonomy and Phylogeny.pptxsharanabasapppa
Deoxyribonucleic acid, a self-replicating material which is present in all living organisms as the main constituent of chromosomes.
DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base.
The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determinesDNA's instructions, or genetic code.
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.
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.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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.
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.
Whole genome duplication and diversification of plant genomes
1. Whole
genome
duplica0on
and
plant
genome
diversity
Simon
Renny-‐Byfield
Department
of
Ecology,
Evolu0on
and
Organismal
Biology
Iowa
State
University
May
12th
2014
2. Outline
• Brief
Introduc0on
• The
role
polyploidy
in
plant
evolu0on
• Repe00ve
DNA
evolu0on
in
polyploids
• Evolu0on
of
gene
duplicates
in
paleopolyploids
• Genome
diploidisa0on
and
frac0ona0on
in
paleopolyploids
• CoMon
fiber
transcriptomics
and
domes0ca0on
3. Introduc0on
• What
is
polyploidy
(whole
genome
duplica0on;
WGD)?
• More
than
a
diploid
set
of
chromosomes
• Allo
vs
auto
• How
to
iden0fy
polyploids?
4. Divergence
0me
(mya)
Introduc0on
• Chromosome
counts
• Age
es0mates
of
duplicated
genes
• Syntenty
analysis
Jiao
et
al.,
2011
Science
Schnable
et
al.,
2011
PNAS
5. • The
greatest
realiza0on
of
the
plant
genomics
era?
Introduc0on
Stebbins
(1950)
–
35%
Grant
(1963,1981)
–
47%
GoldblaM
(1980)
–
70-‐80%
Lewis
(1980)
–
70-‐80%
Current
view
–
100%
of
seed
plants
are
polyploid
6. Three
brief
stories...
① Diversifica0on
of
polyploid
genomes
② Diversifica0on
of
duplicated
genes
following
ancient
WGD.
③ How
polyploids
become
more
diploid-‐like
again,
and
again.
7. 1.
Diversifica0on
of
polyploid
genomes
• Polyploid
genomes
are
highly
dynamic
– How
do
they
vary?
– Over
what
0me
scale?
– Do
different
sub-‐genomes
behave
differently?
8. N.
sylvestris
x
N.
tomentosiformis
2n
=
24
2n
=
24
N.
tabacum
Genome
doubling
2n
=
48
2650 MB per 1C 2650 MB per 1C
5200 MB per 1C
1.
Diversifica0on
of
polyploid
genomes
9. • Es0mate
repeat
content
of
progenitors
and
allopolyploid
– RepeatExplorer
pipeline
– Assess
divergence
of
the
allopolyploid
from
the
diploids
Novak
et
al.,
2010
BMC
Genomics
Renny-‐Byfield
et
al.,
2011
MBE
1.
Diversifica0on
of
polyploid
genomes
10. N.
tom
S4
synthe0c
tobacco
tobacco
N.
tom
Renny-‐Byfield
et
al.,
2012
PLoS
One
1.
Diversifica0on
of
polyploid
genomes
11. WGDs
and
genome
diversity
The paternal (N. tomentosiformis) genome
appears to be underrepresented in tobacco
Renny-‐Byfield
et
al.,
2012
MBE
12. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
S.
C
Harland,
1936
13. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
• Neofunc0onaliza0on
(Ohno,
1970)
• Subfunc0onaliza0on
(Force,
Lynch
and
others)
hMp://www.personal.psu.edu/rua15/Stage3.jpg
17. Renny-‐Byfield
et
al.,
2014
GBE
2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
18. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
Almost
complete
divergence
in
expression
aier
ca.
60
my
Renny-‐Byfield
et
al.,
2014
GBE
19. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
Gene
(G)
effect
Tissue
(T)
effect
G
x
T
interac0on
Renny-‐Byfield
et
al.,
2014
GBE
20. 3.
Biased
frac0ona0on
following
WGD
• What
happens
to
most
genes
following
WGD..
Woodhouse
et
al.,
2010
PloS
Biology
21. 3.
Biased
frac0ona0on
following
WGD
•
CoGe
SynMap
tool
•
Examine
CDS
for
colinearity
with
reference
genome
•
Allows
iden0fica0on
of
duplicated
regions
23. 3.
Biased
frac0ona0on
following
WGD
•
Ten
chromosome
level
comparisons
•
Significant
bias
in
gene
loss
in
all
comparisons
T. cacao
chromosome
G. raimondii
chromosome
(block numbers)
observed predicted !2
p value
2 5 (137,138,139) 929 3641
8 (179,184,185) 642 3641
42.8072 6.1x10-11
6 6 (149,150) 147 2637
9 (190) 580 2637
226.6415 <1x10-15
6 (149,150) 147 2637
10 (33,34,36) 227 2637
15.5573 8x10-5
24. 3.
Biased
frac0ona0on
following
WGD
leaf petal seed
0
200
400
600
count(numberofwins)
LF
MF
Over
expression
of
genes
on
LF
chromosomes
leaf petal seed
−2.5
0.0
2.5
5.0
7.5
−5 0 5 −5 0 5 −5 0 5
log(RPKM MF)
log(RPKMLF)
0.02
0.04
0.06
density
25. 3.
Biased
frac0ona0on
following
WGD
0
2
4
6
−1000 −500 0 500 1000
distance from transcription start/stop site (bp)
meannumberofmappedreads
Most
Frac0onated
Least
Frac0onated
24nt
siRNAs
preferen0ally
locate
to
the
MF
genome
26.
27. Current
project
•
Two
independent
domes0ca0on
events.
•
One
polyploid
and
one
diploid
28. • RNAseq
at
Four
development
stages:
– 5
,
10,
15,
and
20
DPA
• Wild
and
domes0cated
lines:
– Three
in
each
group
• Polyploid
and
diploid
groups:
– Wild
A1,
domes0cated
A1
– Wild
AD1,
domes0cated
AD1
Current
project
29. • Gene
expression
architecture
– How
do
transcrip0onal
networks
alter
(i.e.
similar
to
Swanson-‐Wagner
et
al.,2011)
– connec0vity,
edge
weight,
movement
of
nodes.
– Superimposi0on
of
graphs
to
compare
networks
in
wild
and
domes0cated
(Lelandias
al.,
2006,
Bioinforma0cs)
– Are
there
parallel
changes
in
diploid
vs
polyploid
groups
Current
project
hMp://www.georgebassellab.com/wp-‐content/
uploads/2012/01/seedNet.jpg
30. Conclusions
• WGD
is
ubiquitous
in
angiosperms
• Polyploid
genomes
are
highly
dynamic
• Parental
sub-‐genomes
can
behave
differently
• Gene
duplica0on
(via
WGD)
can
result
in
biological
novelty
• Processes
of
genome
turnover
and
frac0ona0on
result
in
diploidiza0on
• Bias
frac0ona0on
linked
to
expression
and
local
TE
coverage
