PROJECT IN BIOINFORMATICS – KYRIAKOS KOKKORIS

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PROJECT IN BIOINFORMATICS

2006

KYRIAKOS KOKKORIS



HUMAN

AND CHIMPANZEE

WHAT MAKE US DIFFERENT OR
SIMILAR?

COULD WE REALLY KNOW IT
FROM THE GENOME
?






Time Spirals

by Charles Jencks (2000) at Cold Spring Harbor Laboratory




-
A
n overview

about human a
nd chimpanzee genome release.

-
A comparison and analysis of human and chimpanzee genome.

-
Conclusions of these genomes.

-
What are really our similarities and differences? Could we really know?

-
Rhezus macaque
. A non human primate used for the study of hu
man disease (e.g.
HIV)

-
How important can be
the research

for stem cells.

-
Future of genomics.


-
Eth
ical, legal and social issues and general q
uestions
.

A short introduction for human genome project



The human genome project major aims
were many and with

a variable target group.
First of all
,

a huge goal was to

identify

all the approximately 20,000
-
25,000 genes in
human
DNA
. The

determination of
the sequences of

about

3 billion chemical base
pairs that make up human DNA

looks very essential. T
his informat
ion

has to be
stored in databases and

with the appropriate
tools for data analysis

to improve them.

A necessary task was the
transfer

of
related tec
hnologies to the private sector for
further research. Finally, it was very important to
mention

the ethical,

legal

and

social
issues that may arise from the project.


How is genome sequencing done?


-
F
irst

step is to break
into much shorter pieces (
subcloning step
) the chromosomes
that have a range in size of 50
-
250 million bases.


-
Each short piece is
performe
d

as a template to generate a set of fragments that differ
in length from each other by a single base that will be identified
later on
(
template
preparation and sequencing reaction steps
).
See figure 1.

-
The fragments in a set are separated by gel electrop
horesis (
separation step
).

-
Nowadays, n
ew fluorescent dyes are used to allow separation of all four fragments in
a single lane on the gel.

-
We identify the final base at the end
of each fragment (
base
-
calling step
). This
technique recreates the original sequence of A, T, C, G for each short piece generated
in the first step.

-
Multiple rounds of sequencing
are needed to complete a genome
. The chimpanzee
genome draft was based on 3
.5 times lower than the initial publication of other
genomes (human, mouse, rat). However, this draft is so useful for noticing general
differences between the chimpanzee and human genomes

(1)
.






















Figure 1



Sanger sequencing method:

the single
-
stranded DNA to be sequenced is "primed" for replication with a short
complementary strand at one end. This preparation is t
hen divided into four batches, and each is treated with a
different replication
-
halting nucleotide (depicted here with a diamond shape), together with the four "usual"
nucleotides. Each replication reaction then proceeds until a reaction
-
terminating nucleo
tide is incorporated
into the growing strand, whereupon replication stops. Thus, the "C" reaction produces new strands that
terminate at positions corresponding to the G's in the strand being sequenced. (Note that when long strands
are being sequenced the
concentration of the reaction
-
terminating nucleotide must be carefully chosen, so that
a "normal" C is usually paired with a G; otherwise, replication would typically stop with the first or second
G.) Gel electrophoresis
--

one lane per reaction mixture
--

is then used to separate the replication products,
from which the sequence of the original single strand can be inferred.






What information could have from human genome sequence?

Conclusions

from human genome

by the n
umbers



-
The human

genome contain
s 3164.7 million

bases (A, C, T,
and G
).

-
An average number of bases in a gene
are

3000, but sizes
have a big variety.


-
D
ystrophin

is

the largest known human gene
with
2.4 million bases.

-
The total number of genes is
about 30,000. It is much lower compa
ring previous
analysis

(80,000
-
140,000

genes)

that had been based on extrapolations from gene
-
rich
areas as opposed to a composite of gene
-
rich and gene
-
poor areas.

-
About 99.9%

bases are exactly the same in all people.

-
The
unknown
functions are over 50
% of
the
discovered genes.

-
T
he

human

genome
that codes for proteins is around 2% and even less.


-
The
genome

that do no
t

code for proteins is around 50% (‘junk dna)
.

-
S
equences

that are repeated

are

believed

not to
have direct functions, but they
play
e
ssential role

on chromosome structure and dynamics
. As the time pass, these
repeated sequences

resha
pe the genome by rearranging it and create

e
ntirely new
genes, modify and reshuffle

some of the
existing genes.

-
A huge decrease seems to have happened ove
r the last
50 million years

in the rate of
accumulation of repeat
ed sequences

in the human genome

(1)
.


Arrangement of

human

genome


-
The human genome's
regions rich in
gene
s

are predominantly com
posed of the bases

G and C. In contrast,
regions poor in
ge
nes

composed of the bases
A and T.
L
ight and
dark bands on chromosomes

could show through a microscope GC and AT
rich
regions
.

-
Vast expanses of non

coding
DNA

is often exist between regions with high
concentration of genes that appear in random areas alo
ng the genome
.

-
CpG islan
ds are believed to help the regulation

of
gene activity
. CpG islands are

stretched repeated areas

of up to 30,000 C and G bases
in rich

gene

regions

that
form
a bar
rier between the genes and the ‘
junk
dna’.


-
Most
genes

are in c
hr
omosome 1
(2968), and
the less genes are found in
chromosome Y
(231).


Human
genome’s

v
ariations and
m
utations




S
ingle nucleotide substitutions are usually

considered when
determing

sequence
divergence, insertions
-
deletions (indels) and recent duplicat
ions of DNA segments
show a large

proportion of the difference between t
he human and chimpanzee
genomes.

More than
33%
of the indels

are because of repeated sequences
and about
25% of

transposable elements.


There are

about 1.4 million locations where si
ngle
-
base
DNA

differences occur in
humans. This

observation

could lead to very useful conclusions for

finding
ch
romosomal locations for diseases that have been
associated
with
sequences and

give
essential traces

for

human history.


The sequence divergenc
e has a variety among genomic regions because of regional
variations in mutation rate, selective forces and the rate of recombination events
between chromosome pairs during cell division. The highest divergence has been at
the Y chromosome and the lowest a
t the X chromosome. This is normal because the Y
chromosome is present only in
males, which have a higher germ
line mutation rate
than females. In contrast with the X chromosome that is carried in both females and
males.
The ratio of
sperm or egg cell mutat
ions is 2:1 in males comparing with

females.


They could be
several reasons for
this. One given reason is

the greater number of
cell divisions required for sperm formation than for eggs.


Natural selection is believed to
often

occur at the protein leve
l. This is why
nucleotide changes in protein coding regions

are classified into two groups

synonymous changes (no

change in amino acids) and non
synonymous changes
(
change of amino
-
acids)

(1)
.


Pan troglodytes

vs
Homo

sapiens



The publication of
DNA

seq
uence of the chimpanzee genome is an amazing
information for understanding human biology and evolution.


The analysis of chimpanzee (
Pan troglodytes
) and huma
n (
Homo sapiens
) genome
show a
perfect identity of about 96
% of our DNA sequence. The chimpanzee
genome
is an historic achievement that it can lead
to many interesting discoveries

with
implications for human health and not only. The comparison of human genome with
other genomes is a powerful tool for understanding our biological system. The
sequencing

of chimpanzee genome

published on September 2005

and it

is the first
non
-
human primate genome and the fourth mammalian genome

analyzed in a major
scientific publication.

Mouse and rat genome was published on December 2002 and
March 2004. The ‘final’
compl
ete

human sequence published on October 2004

(4
)
.


Differences and similarities of human and chimpanzee genome



Chimpanzees can be described as our closest living evolutionary relatives. This can
teach us many biological differences and similarities betw
een these two species but it
still remains a major question: What make us humans!


The DNA for sequencing chimpanzee
’s

genome was from the blood of a male chimp
named Clint. Unfortunately, Clint died at 2004 from heart failure at
the age of 24
years tha
t is a young age for a chimp to die. Two cell lines have been preserved at the
Coriell Institute for Medical Research in Camden, NJ.



With t
he chimpanzee genome
’s data

is possible

now to determine the ancestral states
of
genetic

variation
s and with the k
nowledge for human genes we might find

evolution signs of

recently

observed

changes

in the last

250,000 years
in human kind
.
S
elective neutrality
,

high frequency

of new variants

and between
-
species divergence
should be corr
elated with the level of within t
he species genetic variation.



C
urrent
research

finds

only six genomic regions that display significantly less
variation than expected from the divergence between
humans

and

chimpanzees that
they

split about 6 million years ago.

T
hese
6
regions
make us be
lieve for

a

recent
positive selection in humans.


Human and chimpanzee genome is found to share many similari
ties that encode the
same proteins. The DNA sequence that can be directly compared of these genomes
has a 99% identity. When, insertions and dele
tions are counted the identity falls to
96%. The identical
amino acid

sequences that
have been encoded from

genes share
29% identity. Human and chimpanzee

species is mentioned to be

diverged
from a
common ancestor
6 million years ago.




Divergence of the

chimpanzee and human lineages occurred about 6 million years ago; the times of lineage
divergence are not to scale.





If we compare with numbers the genetic differences between humans and
chimpanzees is ab
out 60 times less than that is

ob
served betwee
n human
s and mice

and about 10 times less than

that is observed between mice

and rats. The number of
genetic differences between humans and chimpanzees is about 10 times more than
between two humans. Some genes show an unusual quick change in both species
comparing with other mammals. These genes involve mostly

in

perception of sound,
transmission of nerve signals, production of sperm,
and cellular

transport of ions. This
can be a characteristic for primates but it needs a further and more analytical resear
ch.


Humans and chimpanzees have accumulated more deleterious
mutations

over
evolution comparing
with
rodents like mouse. Deleterious mutations are a major
cause of diseases that may cause a specie’s overall fitness. The
se

mutations can lead
us in a concl
usion that primates can be more adaptable in environmental changes and
having a specific environmental adaptation comparing other species.





Despite the similarities between these two genomes we usually try to concentrate in
the differences. The rea
son
s

to distinguish us as human beings
. Around 35 millions
base pairs differ in the two genomes. An average total amount of base pairs is about 3
billions in mammalian genomes. Insertions and deletions cause about 5 million base
pairs differences in non
-
fu
nctional areas. From the above differences, about 3 millions
are

believed to
be in a
n essential protein
coding gene

areas of the genome.


The DNA
fraction that differs

is small but it is the cause of our unique biological
nature.

These differences can s
how us how we walk upright on two feet, why we have
a great enlarged brain, complexity in our language and other

human

features.
The

expected

release of other mammalian genomes in the next years will
be an additional
clue to lead

for the
understanding

of w
hat make us humans.


A few genes in
volved with transcription factors are appeared quicker at humans in
embryonic development comparing with chimpanzees. Around 50 genes are present at
humans without exist or partially deleted at chimpanzees. For example,
genes
involved in inflammation do not appear in chimpanzee genome. One possible reason
can be the known differences between humans and chimpanzees to immune and
inflammatory responses. On the other hand humans appear to have lost caspase
-
12
gene that may p
rotect other species against Alzheimer’s disease.


The comparison of human and chimpanzee genome show deviations from normal
mutation
patterns. These

deviations could occur when a mutation arises in a
population and is so advantageous for the organism th
at it spreads throughout the
population within a few hundred generations and eventually is normally adapted

Six regions

as mentioned above

have been found in the human
genome that has

strong
evidence of selective deviations over the past 250,000 years. One

region contains
abou
t 50 genes, while another one

contains no known genes and

exists in a genetic
area mentioned as ‘gene desert’. T
his

gene desert


may contain elements

that regulate

the expression of a nearby protocadherin gene, which has been
implied
in patterning
of the nervous system.
There is also a

seventh regio
n with genetic information

for
FOXP2

and
CFTR

genes.
FOXP2

gene

has been
involved

for the

characteristic
speech in humans.
CFTR

gene

en
codes a protei
n involved in ion transport and

if

it is
mutated can lead to the

lethal
disease

of cystic fibrosis
. Th
is

gene

is believed to be
a
target

for
positive selection
among

European populations

(3
, 4, 5, and 6
)
.


We share with chimpanzees some common mental functions,

as with some other
species. Our al
most identical dna unfortunately
does

not explain how genes build
minds.
This is why we have to make also a comparison
of animal psych
ology through

evolutionary processes
and genom
ics so we could have a more comp
lete opinion
about dna
and divergence with o
ther species.


The
first
reason why chimpanzees may be
give
n

important information of human
origins is

phyl
ogenetic proximity to humans. A second reason is the

psychological
abilities

of solving social and ecological problems
both human and chimpanzees
.

T
hese abilities can be described briefly

as

foraging, group hunting, food sharing and
intercommun
ity warfare. Consider warfare after f
orty years of observations
in

Africa
have shown that when three or more males from one community find a lone
individual fro
m a
neighboring

community, they

might

kill this individual. This ratio is
meaningful, representing the minimum number of males necessary to hold and kill an
intruder.

Chimpanzees compete with conspecifics both within and between communities. They
can
obse
rve
foreign chimpanzees during boundary patrols, when they make
obvious
incursions into the territories of
neighboring

communities. During these

patrols,
usually take place

by adult males, the chimpanzees
look

unusually silent and wary,
and do not stop to
feed. If they encounter chimpanzees from another community,
big
fights
occur sometimes
.


We have some common thoughts in mathematical level

with chimpanzees and other
animals. However, our capacity to represent large numbers precisely

is unique
.
It

is

not

presently so clear how we have this capacity

but there are interesting

future

possibilities
to explain it genetically
.
Even among human cultures this capacity differs
despite the fact that

language
in these human languages
is as expressive as any other
na
tural language.
A simple question that arise
s

is

how our language

could be
correlated with our thoughts
. One
possible explanation could be
that
some

mechanical
thoughts as mathematics

are affected

by the language faculty

(
2,

7
)
.


Psychology of chimpanzee



A main aspect is if

chimpanzees and other animals have
psychology as

a system of
knowing that enables individuals to infer what others believe, desire and want.

Humans
gradually emerge

these abilities

over the first few years of life
as children

(2,

8)
.


Till

2000 was

believed

that animals, including chimpanzees, l
acked all components
of our

psychology. Povinelli's studies of chimpanzees provided the strongest support
for this conclusion

(9)
.


Hare and colleagues
had a

different experimental approach
.
Hare's studies

result

that
chimpanzees are having with some aspects of human

psychology, but that they are not
unique among animals.
Interesting aspects occur from this experiment like what
is the
nature of the chimpanzees' knowledge of the mental states o
f other chimpanzees
, w
hat
extent is this knowledge a specialization for the domain of competition
,

what ways
could

chimpanzees differ from other animals

and

what specific abilities evolved in
humans to
create

our
unique

psychology, with

our

unlimited capac
ity to represent
others' beliefs a
bout beliefs.

(10,

11)
.


Aspects from
chimpanzee

behavior

and psychology



We
have
notice
d

that we share

with chimpanzees and other ani
mals aspects of
mathematics,
psychology

etc
.

T
he chimpanzee genome will lead to increa
sed capacity
to
exact

homologies

but still

we
can not know how genes build brains

and how the
electrical activity of the brain builds thoughts and emotions.
Quick development of
genetics promise future explanations. Nowadays,
we
begin

to understand the gen
etics
of Williams syndrome and autism

correlated with

psychology.
The properties

of genes
that underlie these disorders, their presence or absence i
n chimpanzees and other
species. T
he
nature of each gr
oup’s psychological limitations connects

genomics and
psychology.


Human

language

is enabled with
Homo

sapiens
’ abilities and computational
thoughts comparing with chimpanzees.

The point is to understand

how the language
faculty
and properties

of the mind
(
storing and recollecting memories
) make

us
more
soph
isticated
, teach and

pass
knowledge through time

(13)
.


The
behavioral

facility
of the chimpanzee is more like
Homo

sapien

s

than any other
species.
But the

psychological mechanisms
on

chimpanzee
behavior

seem
many times

to be
more common with other speci
es
.
That fact conclude
s

that chimpanzees use a
group

of shared psychological capacities to solve differ
ent problems from other
animals and that our genome analysi
s
maybe is insignificant and needs more deep
processes.



C
omparative genomics with

compara
tive neurobiology and
sciences interfere with
behavior

could give

an exact answer in the near future

(12)
.


Rhezus

macaque
. A sec
ond non human primate genome could

lead fo
r
treating human disease as HIV



The R
hesus macaque (
Macaca mulatta
) is the second
non
-
human primate, after the
chimpanzee to have
its

genome sequenced
. T
he rhesus genome

has identical about 92
-
95%
of its sequence with the human
and more than 98%
with the chimpanzee.
So, it
can be obvious that could provide

ideal information for
comparis
ons among the
se

three closely related primates.
Other genomes

of other primates

are on their way for
sequencing like

orangutan, marmoset and gorilla.


The

genetic, physiologic and met
abol
ic similarities with humans from rhesus
macaque give

knowledge

for t
he studies

of human disease
s and it
could serve

for

drug
development.
Rhesus macaques has
essential
role in research for

neuroscience,
behavioural

biology, reproductive physiology, endocrinology and cardiovascular
studies.
Additionally
,
the rhesus

macaque
is

recognized as the best animal model for
human immunodeficiency virus (HIV) infection

because its similar immunodeficiency
virus (SIV).

It also
can provide useful information

to study

other h
uman infectious
diseases and to help

vaccine
’s

research.


The
availability of its genome can give to researchers the appropriate knowledge to
create

a list of rh
esus genes and a list of

differences between r
hesus,
chimpanzee and
human
.
This research is under development and
the National Human Genome
Research Institut
e
(
NHGRI
-

http://www.genome.gov
/
)

has approved such efforts for

biomedical research.


The high quality and valid sequencing

of rhesus macaque genome took almost

two
years to complete and
it
cost
ed

approximat
ely
22 million

US dollars so it is
clearly
obvi
ous that the future analysis of its sequence will lead to very promising and useful
results for humanity

(14)
.




Scott Bateman, National

-

King Features Syndicate



Comparison of
Homo

sapiens with other organisms



-
H
uman's

genome has more

random distrib
ution of
rich
gene

regions. M
any
genomes
of other organisms

are more uniform

with
a more even distribution of these regions.


Humans have
about

three times as many kinds of proteins as the fly or wo
rm. This
difference could be explained because
mRNA transc
ript
alternative splicing

and
chemical modifications to the proteins. This
function

can
give

different protein
products from the same gene.

-
Human genome has a more expanded

number of gene family members

comparing
the same protein familie
s with worms, fli
es, and plants This fact occur mostly

in
proteins involved in development and immunity.

-
The human genome has
more sections
of repeat sequences

around 50%

than the
mu
stard weed (11%), the worm (7%)

and the fly (3%).


What makes us human?



It looks very

complex to give an answer to this question. Although, genomes are
found very similar, there are about 35 million nucleotide differences, 5 million indels
and many chromosomal rearrangements to consider. Maybe these changes will not
have
any significant bi
ological effect but still humans have
uniqueness

as cranial
capacity, bipedalism and advanced brain. The known mutations may result in a large
effect of the current physical and phenotypic differences that separate humans from
chimpanzees and other great
apes.


There are three hypotheses for the evolution of humans: protein evolution
, the 'less
-
is
-
more' hypothesis

and changes in the regions of the genome that regulate gene
activity
.


-
P
rotein evolution:

Amino acid changes could

contribute

to have our uniq
ue
characteristics that are found in rapidly evolving proteins. The role of indels and gene
duplications in human and chimpanzee protein evolution is under consideration but
this field is still not well explored.

-
The 'less
-
is
-
more' hypothesis support
s

tha
t the loss of function changes relative to the
original ape are characteristic of humanity as lack of body hair, preservation of some
juvenile traits into adulthood and expansion of the cranium. Non synonymous
substitutions, indels, loss of coding regions
and deletion of entire genes could cause
t
his

loss of function changes

(15)
.

-
The last hypothesis applies

for the phenotypic differences between humans and
chimpanzees primarily arise from changes in gene regulatory regions. This theory
do
es

not have much

detailed analysis, because it is still very difficult to identify such
regions. Evolution in gene regulating regions is much hard to test. But it looks the
most promising one t
o give us more

information about human biology and evolution

(16)
.


Chimpanzee
’s genome is the most essential addition to the list of sequenced
vertebrate
genomes. It

is the most useful

one

for understanding human biology and
evolution. But stil
l

we need more knowledge and data to answer many questions to
distinguish
Homo sapiens

fr
om the great apes. Better investigation of individual
regions and genes could reveal the details of the patterns that are used at the genomic
level.


Stem cells. A n
ew future of potential research



Many scientists believe that stem cells could change man
y aspects in humanity
.
Diabetics
may not need

insulin, paralyzed
people could walk and we could extend our
life time and many other optimistic options for improvement of life. But can we reach
these possibilities in a short time and without serious difficu
lties and problems?

Huge strides are being made with adult stem cells in conditions like lupus and heart
failure. But the most promising research using embryonic stem cells appears a bit
more troubled.


Stem cells are
very essential

because they can diff
erent
iate

and they can
copy many
times themselves. Most of the other cells can not do that
.
When

a stem cell
turns to

a
muscle or a nerve cell

it can no
t

change back or copy

itself.
That is a reason

whe
n
your spine is
damaged
, it can not be

repair
ed. It is

an irreversible

fact
. Paralysis will
be permanent
. This is why stem cells are very important for
condition
s

that the

cure
needs new cells.
For example i
n our spine the idea
l cure

would be to add back stem
cells which
can be
turn
ed

into nerve cells. Th
e pa
ralyzed
person
could
proba
b
ly

walk
again

(17)
.




There is a d
ifference between ad
ult and embryonic stem cells



Each human has

stem cells. These stem cells are responsible for replacing
‘old’ and
‘tired’
cells in our body.
A given example could be that w
ithout stem cells we could

run out of intestine in a
few

days, our skin in
some

weeks and
our blood in a few
months.


S
tem cells
have a

limited

number in our body

because they can only
be into

some
other kinds of cells. B
lood st
em cells can only become b
lood they could not be
come

nerves. For that reason

we could

not

fix t
he spine with blood stem cells and there is a
limitation to find

many nerve stem cells
until now.


In that case
embryonic stem cells

are useful
. These cells
are found from five days
old

embryos

in a very small size
.
We can find

only 40
-
150 cells at this stage.
This small
amount of cells has to become all of the different tissues that make up a person. So
they turn to any other cell like nerve cells to repair spinal cords.


This approac
h find
s

some ethical problems like encouraging of abortion for many
people.

Many people believe

that most embryonic stem cells come from aborted
fetuses.
But in fact a
borted fetuses are not truly embryonic because they are much
older and most of
these cell
s have turned to a

specific type of cell. Essentially
,

aborted
fetuses

give us adult stem cells
.


Another important

concern is
the idea that to
get embryonic stem cells you have

to
‘use’

an embryo.
People
consider these 40
-
150 cells
as
a
human life, but
is it really?

This work is recently being with

mice

to avoid misunderstandings
.

Some
cells

are taken from a mouse embryo and put

the embryo back
into a female
mouse. This has not still done in humans but it is known that we can take 1
-
2 cells
from an embr
yo
without harming it. T
his procedure called preimplantation genetic
diagnosis (PGD).
It is possible

in the near future,
with

in vitro fertilization
could be
achieved to

donate
some

of thei
r embryo's stem cells to scientific research

and
with
the rest of

t
he embryo's cells to
have a complete baby.


But how can

you turn an adult back into an embryo? You

can

clone him or h
er.
One
possible way

is to take the DNA from the patient and put it into a human egg that has
no DNA.
This

egg would then turn int
o stem c
ells that have the exact identical

DNA
of the patient.


These
stem cells could be made to change

into the type of cells that would b
e put
back into the patient. One simple

example
could be if the patient had a damaged

spine
the
n the stem cells could be c
hanged
to nerve cells.
It is a very difficult
procedure
. We
could not use stem cells from another human for

prevent
ing

rejection.
Each body does

not accept

foreign tissues
added on it. Human

immune systems

prevent this to happen
.
This is why
many drugs are

given to heart and liver transplant patients to inhibit their
immune systems.


While embryonic s
tem cell
research faces

some difficulties
, adul
t stem cell research
has many achievements
. Adult stem cells are being used to treat
diseases as
lupus,
heart
problems,

diabetes
,
leukaemia

and
others
.

It is a future option that stem cell
research could lead in many health solutions but under consideration and overall
thoughts

(17)
.



The future of stem cells should not be scary.



Functional Genomics
.

Is it a
new window to future
?



The
information

of genome data grows
in very rapid way
.
A

new

challenge is the
exploration of how dna

and prote
ins work with each other an
d

environment
al
conditions to create complex

and
dynamic living systems. Systematic studies
will be
focused in a variety of different genomic knowledge.

A spectrum of functional
genomics as
transcriptomics, proteomics, structural genomics, new experimental

techniques
, and comparative genomics

help

in a very large scale

the future of genetic
sciences
.

-
Transcriptomics

occur with the analysis of messenger RNA

transcribed from active
genes to follow when, where, and under what conditions genes are expressed.

-
Proteomic
s are based on the studies of

protein expression and function
. Proteomics
try to explain what exactly happens
in the cell

and they have

big

applications to drug
design.

-
Structural genomics

are being worldwide a very interesting area for the 3
D

structures
of one or more proteins from each protein family
. These studies also offer

clues to
function and biological targets for drug design.

-
New e
xperimental methods

are taken place

for understanding the function of DNA
sequences and the proteins the
y encode
,

include
knockout studies

for inactivation of

genes in living organisms and monitor any changes that could reveal their functions.

-
Comparative genomics

is the analysis of
DNA

seque
nce patterns of humans and well
studied model organisms in
many d
etails. It can be used

as a powerful strategy

for
identifying human genes and interpreting their function.


Applications, Future Challenges





The

knowledge from the DNA sequence will define research through the coming
decades to
make us
understand

the

b
iological systems. This enormous

and difficult
task

will require

the effort of many

scientists from

both the public and private sectors
worldwide.


The draft sequence
is already resulting

to
find genes associated with disease
s
.
Many
genes have been ident
ified to have an association
with breast cancer, muscle disease,
deafness, blindness

etc
. Additionally,
exploring

the
dna

sequences
associated with
diseases as cardiovascular disease, diabetes, arthritis, and cancers is being ai
ded by
the human variation m
aps

generated in the
human genome project

in cooperation with
the
private sector.
This

information
provides

specific

targets for the development of
effective new therapies.


A
new approach to biological research

occur
s

day by day with additional knowledg
e
about human genome and othe
r

organism’s

genome
.
Nowadays, whole
genome
sequences and
modern
technologies, they can
answer questions in a very quick and
right way. The
study

of all the genes in
genome

give information

how have been
interacted, regulated,
expressed, related under the right guidance and the future
knowledge given could make us organise and understand

the chemistry of life.




Social, ethical and legal c
oncerns
of g
enetics

and general questions


-
What will be the u
se of genetic information

by

insurance companies, employers
,
courts, military services etc?

-
Who can have access to personal genetic information, and how
this

information can
be used?




Scott Willis, San Jose



The San Jose Mercury News



-
What are the limits of p
rivacy and access
of the

genetic information?

-
Who can make right
dec
isions and control
this

genetic information?


-
What will be the d
iscrimination of people

due to
genetic differences?


-
How
could
the society
categorise

people through
the
individual
DNA
?

-
What will be the

affect in minority communities?




-
Do healthcare
employees can handle proper
ly the genetic knowledge that
is

provided
?

-
Is it reliable enough
this

genetic information?



-
What
are

the

accuracy, reliability and utility

of genetic tests
?

-
Who would
regulate
this

information?

-
Is it prepared properly

the public
for new genetic issues
?



Randy Bish, Pittsburgh, PA

-

the Tribune
-
Review



-
How much uncertain is the fact that genetic knowledge
change quickly and
how
much

valid

and safe information provid
e

without a

long
period of

testing?

-
What are the limits

of human free will for science?

-
How sure is that

genes
could
make
people to

behave in a particular way?


-
Could we control human character

through genetics
?




Nick Anderson, Kentucky

-

The Louisvi
lle Courier
-
Journal



-
How safe are genetic modified
foods
for

humans?


-
What is the effect on environment?


-
What will be the accessibility of
DNA

information for developing products and cure
diseases?

-
Could someone really own genes and
DNA
?





Vic Har
ville, Little Rock, Arkansas



The Arkansas Democrat
-

Gazette



















As a conclusion…



What is the difference between modern human, the great apes and earlier hominids?
In what hominids and when in evolution did essential and unique physical
traits and
behaviours appear? How and where in our brain do human’s specific capabilities
exist? The genetic mechanisms
may

give an answer of formation and evolution of
these questions. Analysis of the human genome and that one of our closest relative,
chi
mpanzee, with additional information from other genomes could discover the
genetic basis of the physical and behavioural traits that distinguish us from apes and
other organisms.

It is a very difficult task with different issues that
it
should be
studied u
nder deep consideration.


Nowadays, it seems just the beginning of a large, complex and very thoughtful
challenging story for exploring human’s past, present and future horizons.


References


1.Sean

B.

C
aroll
,

Genetics and the making of
Homo sapiens
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Nat
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Hsiung Li and Matthew A. Saunders,

The chimpanzee and us
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437,
50

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M Hauser,

Our chimpanzee mind
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4.

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himpanzee
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Povinelli, D. J. & Eddy, T. J. What youn
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68
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2
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Emery, N. J. & Clayton, N. S. Effects of experience and social context on
prospective caching strategies by scrub jays.
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414
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Jeffrey Rogers
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and George
M.

Weinstock
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