Fossil-soft tissue-the fossilized bone treatement-remove mineral content from the fossilized bone-marrow cavity -structures such as blood vessels, bone matrix, and connective tissue (bone fibers)
Boxes along the wall r automated gene sequencers
Actual structure of s smaalll fragment of DNA of diano
If we looked at a screen like dis once a second – 8 hours a day – more dan 2 years – big sequence
Shotgun sequencing dispenses with the need for mapping and so is much faster. It involves chopping the DNA into fragments of size c. 2000 base pairs(bps) and 10000 bps, sequencing the first and last 500 bps of each fragment. It then uses computer algorithms to assemble the entire sequence from the sequenced fragments.
Dna fragments wid points of restriction enzymes located
The enzymes r chosen by d computers
The dark parts r the restriction fragments
Its like putting a puzzle together
Guar-an endangered speciesIn real life, one of the most anticipated targets for cloning was once the Woolly Mammoth, but attempts to extract DNA from frozen mammoths have been unsuccessful.a cow named Bessie gave birth to a cloned Asian gaur, an endangered species, but the calf died after two days. In 2003, a banteng was successfully cloned, followed by three African wildcats from a thawed frozen embryo. the Pyrenean ibex mentioned above was cloned, at the Centre of Food Technology and Research of Aragon, using the preserved DNA of the skin samples from 2001 and domestic goat egg-cells. (The ibex died shortly after birth due to physical defects in its lungs.)  One of the continuing obstacles in the attempt to clone extinct species is the need for nearly perfect DNA.
. Guar are a near-extinct species of Ox. Noah was born from a regular cow egg with Guar cells fused inside.Dolly was the first successfully cloned mammal from an adult cell.Noah ,a first endangered animal, a Guar to be cloned .A flower that last bloomed when saber-toothed cats roamed the Earth is once again alive and growing. Russian scientists say they've dug up remnants of a 32,000-year-old plant from Siberia's frozen wasteland and successfully cloned 36 more of them from its fruit tissue, the New York Times reports.A technique pioneered in 2008 successfully cloned a mouse from the cells of a mouse frozen for 16 years, A technique pioneered in 2008 successfully cloned a mouse from the cells of a mouse frozen for 16 years, and the professor believes he can use the same technique to resurrect the mammoth, which has been extinct for 5,000 years.One of of the world's first two cloned wolves has died due to unknown causes, reports the Korea Times. Snuwolf, 4, was found dead at South Korea's national zoo. Her identical sister, Snuwolffy, remains healthy. "Snuwolf had been in good condition," said Prof. Shin Nam-sik, The buffalo has now joined sheep, camels, and wolves among the ranks of the cloned,
As you may have surmised from the above definitions, it doesn’t necessarily follow that an ectothermic reptile literally has colder blood, temperature-wise, than an endothermic mammal. For example, the blood of a desert lizard basking in the sun will temporarily be warmer than that of a similar-sized mammal in the same environment, though the lizard’s body temperature will drop with nightfall.Anyway, in the modern world, mammals and birds are both endothermic and homeothermic (i.e., “warm-blooded”), while most reptiles (and some fish) are both ectothermic and poikilothermic (i.e., “cold-blooded”).. So what about dinosaurs?Because there are no living dinosaurs around to be dissected (with one possible exception, which we’ll get to below), most of the evidence for warm-blooded metabolism stems from modern theories about dinosaur behavior. Here are the five main arguments for endothermic dinosaurs (some of which are challenged below, in the "Arguments Against" section).At least some dinosaurs were active, smart, and fast. As mentioned above, the main impetus for the warm-blooded dinosaur theory is that some dinosaurs exhibited “mammalian” behavior, which entails a level of energy that (presumably) can only be maintained by a warm-blooded metabolism.Dinosaur bones show evidence of endothermic metabolism. Microscopic analysis has shown that the bones of some dinosaurs grew at a rate comparable to modern mammals, and have more features in common with the bones of mammals and birds than they do with the bones of modern-day reptiles.Many dinosaur fossils have been found at high latitudes. Cold-blooded creatures are much more likely to evolve in warm regions, where they can use the environment to maintain their body temperatures. Higher latitudes entail colder temperatures, so it’s unlikely that dinosaurs were cold-blooded.Birds are endotherms, so dinosaurs must have been too. Many biologists consider birds to be “living dinosaurs,” and reason that the warm-bloodedness of modern birds is direct evidence for the warm-blooded metabolism of their dinosaur ancestors.Dinosaurs’ circulatory systems required a warm-blooded metabolism. If a giant sauropodlike Brachiosaurus kept its head in a vertical position, like a giraffe, that would have put enormous demands on its heart--and only an endothermic metabolism could fuel its circulatory system.ConsAccording to a few evolutionary biologists, it’s not enough to say that because some dinosaurs may have been faster and smarter than previously assumed, all dinosaurs had warm-blooded metabolisms--and it’s especially tricky to infer metabolism from presumed behavior, rather than from the actual fossil record. Here are the five main arguments against warm-blooded dinosaurs.Some dinosaurs were too large to be endotherms. According to some experts, a 100-ton sauropod with a warm-blooded metabolism would likely have overheated and died. At that weight, a cold-blooded dinosaur could have been what’s called an “inertial homeotherm”--that is, it warmed up slowly and cooled off slowly, allowing it to maintain a more-or-less constant body temperature.The Jurassic and Cretaceous periods were hot and muggy. It’s true that many dinosaur fossils have been found at high altitudes, but 100 million years ago even a 10,000-foot-high mountain peak might have been relatively balmy. If the climate was hot year-round, that would favor cold-blooded dinosaurs that relied on outside temperatures to maintain their body heat.We don’t know enough about dinosaur posture. It’s not certain that Barosaurus elevated its head to forage for grub; some experts think large, herbivorous dinosaurs held their long necks parallel to the ground, using their tails as q counterweight. This would weaken the argument that these dinosaurs needed warm-blooded metabolisms to pump blood to their brains.The bone evidence is overrated. It may be true that some dinosaurs grew at a faster clip than previously believed, but this may not be evidence in favor of a warm-blooded metabolism. One experiment has shown that modern (cold-blooded) reptiles can quickly generate bone under the right conditions.Dinosaurs lacked respiratory turbinates. To supply their metabolic needs, warm-blooded creatures breathe about five times as often as reptiles. Land-dwelling endotherms have structures in their skulls called “respiratory turbinates,” which help retain moisture during the respiration process. To date, no one has found conclusive evidence of these structures in dinosaur fossils—hence, dinosaurs must have been cold-blooded (or, at least, definitely not endotherms).
Chickens as model systemsHistory of use
1>it is fairly well-accepted by the scientific community that birds are a special lineage of theropod dinosaurs.2>SO THOUGHT OF BIOLOGICAL MODIFICATIONS TOOL WERE CONCIEVED.3>2>
1>MOLECULAR GENETIC MANIPULATION TECHNIQUES2>This window not only allows you to observe the embryo as it grows, but it also allows you to manipulate something
Building Dinosaurs: AMolecular Genetics Case Study
Approaches-Genetics and the Gen.Engg. tweak DNA Sample? Yes No CLONING! ENGINEER!
History-The Research So Far…• Dinosaur fossils have been known for millennia, although their true nature was not recognized- great fossil lizards• 1842-English paleontologist Richard Owen coined the term "dinosaur”. Distinctive features-Distinct taxonomic group.• Dinosaur mania-Bone Rush-Post 1897-Antarctica Fossil Search.
• Current dinosaur "hot spots" include southern Africa, South America (especially Argentina) and China.• China -exceptional feathered dinosaur specimen 1. Unique geology of dinosaur beds 2. Arid climate-conducive to fossilization.
EXTRACTING MULTIPLY DNA DNA SEQUENCING & FILLING GAPS SYNTHESIS &CLONING! TESTING
EXTRACTION OF DNA• Fossil-soft tissue-Bone marrow cavity, blood vessels, bone matrix, and connective tissue (bone fibers)• Fossilized bone treatment-LOY’S antibody extraction technique-20% of proteins recovered-bad yield for sequencing• March 2005-actual soft tissue inside a 68-million-year-old Tyrannosaurus rex leg bone from the Hell Creek Formation in Montana.• Mosquito fossils-nucleated RBCs
Identifying the extracted DNATHIS IS DONE WITH THE HELP OF CRAY XMP SUPERCOMPUTERS ….
• Dat sequence – just codes for 1 protein• 3 billion such sequences• Thanks to these superfast super computers !!! The X-MP CPU has brillant speed of 9.5 nanosecond clock cycle this makes the identification process a walk in a park
Error in d sequence• D extracted one is fragmented• First thing – REPAIR IT
Sequence assembly using mapping• Originally sequencing was performed by cutting the chromosomes into large pieces which were cloned into bacteria, creating a whole library of DNA segments.• The segments were cut open to look for common sequence landmarks in overlapping fragments. These were used to fingerprint the fragments, so that it was known where in the chromosome the fragment was- this is called mapping.• The fragments were cut into smaller pieces and the process repeated and the small fragments were sequenced. Finally the whole sequence is known (in terms of short fragments and their locations on the chromosome).
• with d help of XMP - cuts d DNA with the help of restriction enzymes - Computer itself selects d enzymes (from data bank)
• 2 enzymes cut on either side of the damaged point• Know wat pairs should be inserted to repair d injury• align various cut fragments , like so
• Find a fragment of DNA dat overlaps the injury area• Computer now recombines them by searching for overlapping sections of code
TESTING THE GENE• Unknown if those sequences are really functional.• One base pair off-non functional gene• Transfection• Dr. Chang and his team successfully used this method to test a Triassic archosaur gene
History of cloning …The first cloning was done in sheep.An Asian Gaur was cloned from a cow, but it died after 2 days.Now a days buffalos are also cloned for better milk production.In 2008 a successful cloned mouse is produced using cells of mouse frozen for 16 years.Two wolves were cloned,one of them has died due to unknown causes, as reported by the Korea Times. 32,000 year old plant from Siberias frozen wastel,Sylene stenophylla regenerated from tissue of fossil fruit , as reported by the New York Times.
Cloning Cloning is the process of making a genetically identical organism through nonsexual means. www.youtube.com/watch?v=hepoJgGJtNc https://
Cloning of dinosaurs• Cloning of a dinosaur can be achieved by taking into account that they resemble modern birds and reptiles.• Few theories support reptiles as the descendants of dinosaur• Charles Darwin’s origin of species suggested that there was greater amount of skeletal similarities between dinosaurs and modern birds. Also the researchers analyzed its thigh bones and found out transparent and hollow blood vessels.The vessels are similar in all respects to blood vessels recovered from the bones of modern ostriches.
How to choose an egg cell??Species with similarities with dinosaurs e.g: feathers, claws, oviparous ,warm-bloodedShould be able to nourishConditions favoring its developmentSpace managementSpecies which makes a good model systemhttps://www.youtube.com/watch?v=zP2m95JAD4g
Limitations Dinosaur DNA is difficult to obtain and to sequence.Even if researchers did find a perfectly preserved mosquito with a body full of dinosaur blood,retrieving its DNA would still be difficult.Even if we have the DNA sequenced, there will be some gaps that must be filled.After sequencing it should be inserted into oocyte of the same organism which is impossible.Wouldnt work to insert the DNA into reptiles ova because species’s ova is specialized for thatspecies alone.Even if any reptiles ova could hold dinosaur DNA, a problem still arises with the developmentof the dinosaur embryo.
How many of you have watched “Jurassic park”??How many of you have dreamt of peering out the window of an SUV and watch a T-rex lumber into a clearing?? Deep inside you, theres a hole that can only be filled by pointing a Canon PowerShot at a diplodocus!!
Dilemma of Jurassic park!!• prehistoric mosquitoes trapped in amber (fossilized tree resin) with dinosaur blood in their bellies!!! problem-:- DNA preserved in amber degrades over several million years. If fragments ofdinosaur DNA survived the passage of time, they might mix with insect DNA duringextraction.• problem of missing DNA !!• way to transform the DNA into chromosomes !!• find a place to implant them? .. living dinosaur egg..?!?! Don’t give up hope just yet…
So..the answer does not lie in dead mosquitoes or preserved eggs...it lies in.. Maybe..
But why do they don’t look alike even a little bit??
But why do they don’t look alike even a little bit??
But wait there is more to this than meets the eye…The word is… • Atavism is the tendency to revert to ancestral type. • an atavism is an evolutionary throwback, such as traits reappearing which had disappeared generations before. • when genes for previously existing phenotypical features are preserved in DNA, and these become expressed through a mutation that either knock out the overriding genes for the new traits or make the old traits override the new one. • traits that have disappeared phenotypically do not necessarily disappear from an organisms DNA. The gene sequence often remains, but is inactive.
REVERSE GENETICS• is an approach to discover the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing• The regulatory genes—the master switches of development—contain the recipes for making certain proteins that stick to different stretches of the genome.• These regulatory genes function as a brake shoes, controlling at what time during development, and in what part of the body, other genes get turned on.• So making a chicken egg hatch a baby dinosaur should really just be an issue of erasing what evolution has done to make a chicken• Trick is to learn how to control the control genes.• Some of the evidences that chicken are descendants of dinosaurs are given in the following slides in the form of picture.
This tail get resorbed during embryonic development withthe help of controlling factors, if we could shut these factorsoff, we could get a chicken with a “TAIL”.
• Bird hands skeleton differs from that of our dinosaurs species, because that hand is a wing.• But during embryonic stage of a chicken it was found that hand resembles that of archaeopteryx.• During embryonic stage ,some genes get turned on and fuses the finger together.• So we are looking for that gene.
OVERVIEW FOR “CHICK” EXPERIMENT• you need a chicken embryo, This is basically just an undeveloped egg that you know has been fertilized.• remove part of the shell to create a window onto the embryo,• Window should be covered, keep the egg under sterile conditions, the embryo will continue to grow normally.• extra genetic material, such as a gene sequence that codes for a protein called a “transcription factor", is introduced, , it will be read by the cells there and the transcription factor protein will be produced.• When a transcription factor changes the expression of certain genes during embryonic development, this can have a potent effect on the way an embryo is shaped.• These shape-controlling genes, can be either turned on or off,• Transfection is when you introduce nucleic acids (extra DNA or RNA) that will disrupt expression of a certain gene.• . To perform transfection, scientists create transient holes in the cell membranes of the chick embryo, through which the genetic material can pass.• These holes can be created chemically, with calcium phosphate or cationic lipids• When these holes open up, the genetic material can pass into some of the embryo’s cells and, with some luck, will become incorporated into the animal’s nucleus. There, they will control the expression of the chicken embryo genes.
After all the story… What purposes could cloning serve?
A Buisness Perspective..• Zoos with these creatures could easily charge hundreds of dollars per visitor.
Natural Selection Perspective• Cannot adapt to changing ecological and climatic conditions
Philosophical Questions• Do long-extinct species gain anything from being brought back from the dead?• Is it cruel to place these animals in ecosystems different from the ones they evolved in?• If this is so, and modern plants and animals take precedence, will we be forced to slaughter the very creatures we resurrected? What about our own Pleistocene antecedents?
• Sure, we might be able to clone animals, but the prospect of being hunted by an ancient predator is less important than the other questions mentioned above. Before we clone the first mammoth, we should carefully examine the reasons why we are doing so. If it is only another way to exalt human arrogance or pad the wallets of a few, I would argue that Pleistocene mammals are better off dead.• Will some Pleistocene species outcompete and force some modern species into extinction?
To Sum It Up…• Tackling a problem in Genetics-defining the problem to manipulating existing procedures to devising new procedures!• Defined the challenges-unique problems, unique challenges!• Realized the interdisciplinary nature of Genetics-Paleontology and Archeology, Computer Science, Mathematical Modeling, Ecology, Bioengineering and the list goes on…
REFERENCES-The best of few!• Roger Bunburg et all-”The Chickenosauras Revolution”-Nature, May 2007 issue• “Scientist Vows To Reverse-Engineer Dinosaur From Chicken”-Stuart Fox et all,The Popular Science Magazine(March 2010)• “Why Do We Keep Going Back to Jurassic Park?”-Geoff Spencer, Researchers Compare Chicken, Human Genomes, National Institute of Health News, December 8, 2004• Ryan Whitwam (2012). Sorry, you will never ride, see or pet a cloned dinosaur• Chang and team (2002). Recreating a Functional Ancestral Archosaur Visual Pigment, Mol. Biol. Evol., Volume 19(9).• “How to build a Dinosaur”-Jack Horner et all (2003)• “Jurassic Park”-Michael Chirchton,1990