Tuesday, April 24, 2012

DNA - MORE OR LITTLE - CAN BE BAD ?

DNA - MORE OR LITTLE - CAN BE BAD ?

There's added array to DNA than you ability think: Deletions or additions of abiogenetic actual amid individuals, alleged archetype cardinal variations (CNVs), are a accepted antecedent of abiogenetic diversity. Now, basic assignment appear actuality today at the American Society of Human Genetics affair suggests that men who accept added CNVs than boilerplate may be added acceptable to afford accouchement with the eye blight retinoblastoma. The analysis reflects growing activity amid geneticists for CNVs, a blazon of abiogenetic aberration that hadn't gotten abundant absorption until afresh but that's now actuality affiliated to a cardinal of diseases.

All youngsters who advance retinoblastoma in both eyes affiliated a abnormal gene that acquired the disease. But in 80% of these cases, neither ancestor carries the mutation. Somehow it arose in the father's sperm. No one knows how this happens, but advisers accept speculated that some fathers may be added afflicted to DNA accident than others. At the University of Pennsylvania (U Penn) and the Children's Hospital of Philadelphia, advisers accept spent about 7 years accession cases of this attenuate blight and acquisition DNA from accouchement and their parents. They are additionally inquiring about a ambit of ecology exposures that may accept afflicted fathers, but that advice isn't yet available.

The abiogenetic findings, however, are boring advancing together. At the meeting, geneticist Elizabeth Chao, a postdoctoral adolescent at U Penn alive with geneticist Arupa Ganguly, declared DNA taken from 169 fathers whose accouchement developed the disease. They articular 37 CNVs they advised large--greater than 500,000 DNA bases--and in accepted begin that the fathers had added CNVs than controls, about eight on boilerplate adjoin three. Twenty-one dads had no apparent CNVs at all, but Chao suspects this may be due to the technology used, which has adversity acrimonious up actual baby stretches of DNA that are bifold or deleted.

Particularly absorbing were CNVs in genes that assure adjoin DNA damage, such as the breast blight gene BRCA2. Chao doesn't apperceive whether these CNVs are affiliated by the fathers from their own parents or whether they accrue with age. And it's too aboriginal to say how or alike whether CNVs accord to the accident of a mutated retinoblastoma gene. One possibility, says Chao, is that aerial numbers of CNVs somehow account DNA accident by authoritative dads beneath able to assure themselves from ecology blame such as radiation. Another account is that the CNVs are aloof "markers of a beneath abiding genome," suggesting that these men are added accessible to DNA accident generally. The fathers aren't at college accident of blight themselves, Chao adds.



Although these dads are healthy, the allegation are agnate to those in added diseases angry to aerial CNV levels. For example, booty Li-Fraumeni syndrome, a abiogenetic action that leads to a cardinal of cancers. In assignment appear in August in the Proceedings of the National Academy of Sciences and presented today, advisers from the Hospital for Sick Children in Toronto, Canada, advised 11 families with Li-Fraumeni affection and appear that those afflicted had an boilerplate of 12 CNVs in their genome, compared with three in controls. Added assignment declared an added accountability of CNVs in schizophrenia, decidedly in DNA that's allotment of a gene.

The retinoblastoma assignment is "very preliminary," says geneticist Stephen Scherer of the Hospital for Sick Children, who alternate in the Li-Fraumeni study. In general, CNV abstracts are "getting abundant better," but the assignment is still arduous because altered technologies crop altered copy-number variants. "It's really, absolutely tricky" both to accurately analyze CNVs and to actuate their appliance to disease, he says. Still, says Scherer, identifications of large, attenuate CNVs are acceptable to be accurate, and the access is alms new achievement in pinpointing DNA that's active disease.

Sunday, March 18, 2012

Gene? What is that? DNA or Chromosome?

Gene? What is that? DNA or Chromosome?

Gene(Greek genos "birth, race”) is basic unit of heredity found in the cells of all living organisms, from bacteria to humans. Genes determine the physical characteristics that an organism inherits, such as the shape of a tree’s leaf, the markings on a cat’s fur, and the color of a human hair etc. That is the gene which is responsible for right handed and left handed character of individuals.

Genes are composed of segments of deoxyribonucleic acid (DNA), a molecule that forms the long, thread like structures called chromosomes (if you are interested, please notify me, I’ll write you about composition, structure and function of DNA). The information encoded within the DNA structure of a gene directs the manufacture of proteins, molecular workhorses that carry out all life-supporting activities within a cell.

Chromosomes within a cell occur in matched pairs. These can be seen on dividing cells under light microscope. Each chromosome contains many genes, and each gene is located at a particular site on the chromosome, known as the locus. Like chromosomes, genes typically occur in pairs. A gene found on one chromosome in a pair usually has the same locus as another gene in the other chromosome of the pair, and these two genes are called alleles. Alleles are alternate forms of the same gene. For example, a pea plant has one gene that determines height, but that gene appears in more than one form—the gene that produces a short plant is an allele of the gene that produces a tall plant. The behavior of alleles and how they influence inherited traits follow predictable patterns. Austrian monk Gregor Mendel first identified these patterns in the 1860s.

In organisms that use sexual reproduction, offspring inherit one-half of their genes from each parent and then mix the two sets of genes together. This produces new combinations of genes, so that each individual is unique but still possesses the same genes as its parents. As a result, sexual reproduction ensures that the basic characteristics of a particular species remain largely the same for generations. However, mutations, or alterations in DNA, occur constantly. They create variations in the genes that are inherited. Some mutations may be neutral, or silent, and do not affect the function of a protein. Occasionally a mutation may benefit or harm an organism and over the course of evolutionary time, these mutations serve the crucial role of providing organisms with previously nonexistent proteins. In this way, mutations are a driving force behind genetic diversity and the rise of new or more competitive species that are better able to adapt to changes, such as climate variations, depletion of food sources, or the emergence of new types of disease.

Geneticists are scientists who study the function and behavior of genes. Since the 1970s geneticists have devised techniques, cumulatively known as genetic engineering, to alter or manipulate the DNA structure within genes. These techniques enable scientists to introduce one or more genes from one organism into a second organism. The second organism incorporates the new DNA into its own genetic material, thereby altering its own genetic characteristics by changing the types of proteins it can produce. In humans these techniques form the basis of gene therapy, a group of experimental procedures in which scientists try to substitute one or more healthy genes for defective ones in order to eliminate symptoms of disease.

Genetic engineering techniques have also enabled scientists to determine the chromosomal location and DNA structure of all the genes found within a variety of organisms. In April 2003 the Human Genome Project, a publicly funded syndicate of academic scientists from around the world, identified the chromosomal locations and structure of the estimated 20,000 to 25,000 genes found within human cells. The genetic makeup of other organisms has also been identified, including that of the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, the roundworm Caenorhabditis elegans, and the fruit fly Drosophila melanogaster. Scientists hope to use this genetic information to develop life-saving drugs for a variety of diseases, to improve agricultural crop yields, and to learn more about plant and animal physiology and evolutionary history.

Here are some pictures, these might helpful to understand undoubtedly.






1.Nucleotides,
2..DNA
3.Genes
4.Chromosome
5.Cell
6.Body

DNA Translation

DNA Translation

What is it?
DNA translation converts the mRNA sequence into amino acids that form protiens. This creates most of the protiens that make up cells. It creates the last step from DNA to a protien.
Wher does it occur?
Translation occurs outside the nucleas also known as in the cytoplasm. Eventhough this is true one article suggests that translation can occur inside the nucleas. Click here to see.
When does it occur?
Translation occurs right after transcription is done and the mRNA is transported out of the nucleas.
How does it Happen?
During DNA translation, messenger RNA, transfer RNA, and ribosomes work together to produce proteins. A ribosomal subunit attaches to a mRNA molecule. The Transfer-RNA transports the amino acid from the cytoplasm to the ribosome. The start codon attaches to Met this starts making the protein.

Genetic Variations - Mutations

Genetic Variations - Mutations

This is a complicated topic and I want to keep a record of what I learnt in school (and various other programs, materials) and also from related research. By writing it down I believe I understand the concepts better and additionally it allows me to refresh the concepts quickly.

This is sixth of my series on the quest for "Theory of Convergence" and second topic on genetics. This topic speaks to convergence of multi-discipline such as - biology, life, economics, environmental science, human studies, nature, design thinking, physics, chemistry, etc.
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As you may recall, from my earlier blog (Dec 31st 2010)  - "Basics of genetics" I had introduced the topic of Genetic mutations (Please read that topic again as a refresher). Well here we are getting back to the grind after a long hiatus from this topic. Unlike my other blogs, mutation topic will mostly be academic in nature.
Genetic variation is fundamental to evolutionary change. There are 3 types of genetic variations - Mutations, gene flow and sex.

    We will be discussing mutation in greater detail below,
    Gene flow is movement of genes from one population to other,
    Sex introduces new gene combinations in to population.

Gene flow occurs due to an event such as pollen dust migrating through the air to another set of plants or you can think of gene flow as people migrating from one part of the world to another. With out gene flow - there is less evolution, therefore less diversity. Less diversity means less innovation/creation. Gene flow has been the center of USA's innovative capabilities. USA's population was created on the basis of acceptance of people of all color, creed, etc. This has turned out to be the greatest asset of USA and has resulted in the land of great creativity & innovation. Innovation is not limited to gadgets such as iPads and iPhones, but creativity is extended to all fields including social, legal, arts, science, public policies, etc.  That fits right in to the theory of convergence. Isn't this getting exciting !!! Well I am getting excited and possibly digressing from the subject a bit. Back on topic.....
Sex is an important source of genetic variation. Organisms reproduce through sex and parent genes mixes resulting in an offspring that has genes from both the parents. For example, an offspring may inherit blue eyes from mom and big nose from dad. This shuffling of genetic variation is important for evolution but as you may imagine it can render some characteristics obsolete.

Mutation
Mutation is a change in DNA, the hereditary material of life. As noted in earlier blog, DNA affects how an organism looks and functions. Mutations of DNA are widely believed to be random, at this time. Some day science may prove it otherwise, until then we will stick to what we know so far. The mutations in DNA is the result of such diversity of life on earth. Mutations over 4 billion years have created fantastic creatures such as parasites, elephants, lions, apple, jelly fish, octopus, shark, redwood trees, apples, etc. There you go - that is 4 billion years of experimental results for human to analyze.

In fact I believe mutations are a classic example that humans can use in all aspects of our lives - Note this important comment for future - We will discuss this detail in later topics. Mutations and exaptations are marvels of natures innovation. I guess it is now time to explain exaptation (courtesy - http://evolution.berkeley.edu/evosite/evo101/IIIE5cExaptations.shtml)

    Exaptation—a feature that performs a function but that was not produced by natural selection for its current use. Perhaps the feature was produced by natural selection for a function other than the one it currently performs and was then co-opted for its current function. For example, feathers might have originally arisen in the context of selection for insulation, and only later were they co-opted for flight. In this case, the general form of feathers is an adaptation for insulation and an exaptation for flight.


Darwin never knew this, he understood that species adapt and change, but he did not know understand the actual process. Thanks to the discovery of DNA we now know how evolution works.

First of all it is important to note that not all mutations matter to evolution. Some mutations are not passed on to the off-spring.  (courtesy -  http://evolution.berkeley.edu/evolibrary/
For example, the golden color on half of this Red, Delicious, apple was caused by a somatic mutation. The seeds of this apple do not carry the mutation.
The only mutations that matter to large-scale evolution are those that can be passed on to offspring. These occur in reproductive cells like eggs and sperm.

Some mutations are positive and some are negative - that is the beauty of nature - Nature is experimenting all the time. For example some mutations cause an organism to develop cancer and some may cause an organism to develop legs instead of fins (which is what is believed to have been the first land animal).
In early 2000's scientists were studying stickle back fish in a lake in British Columbia (West Canada). They were particularly interested in how they had evolved. Ocean stickle backs had spikes & the the fresh water ones did not have any spikes. This was a mystery they intended to solve. They noticed that the lake stickle back fish had a trace of bones ,one small and one big, where the spike would have been there. On further study (which we will talk about, later under the topic "Epigenome") they concluded that a particular gene had mutated.

Types of mutations

There are many ways a DNA can change. As you may know in human body - DNA is made of base pairs A, C, G & T. There are six billion base pairs in human genome.  These are being constantly copied and replicated during a human's life time. Hence mathematically the possibility of error is large. However the nature has been kind to life and such mutations (or errors if you want to call them that) are rare.

Some of the main types of mutation are substitution, insertion and deletion. Substitution occurs when one letter in DNA is substituted with another (for example A is replaced by G - may occur during copying). Insertion occurs when extra base pairs are inserted in to the chain. Deletion is just that deletions - deletion of base pairs.

Causes of mutations

Mutations occur mostly when cells divide and DNA makes a copy of itself. Sometime the DNA fails to copy and there is small difference in DNA sequence. We are talking really small changes here. Human genome has 6 billion base pairs, and any base pair letter can change during copying.

Another main reason for mutation is the external factors such as environment. For example exposure to chemicals such as DDT, can cause DNA to breakdown and when cells repair themselves it might not be perfect. I have friends who were running behind trucks (when they were kids) that was spewing DDT to kill mosquitoes in cities - Sad isn't it - At that time we did not know the ill effects of DDT. Thanks to genetic research, DDT is now banned all over the world.
From: http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_04Following cell division, the copied DNA is imperfect

Effects of mutations
Mutations usually has negative connotation. However mutuations have both positive and negative effects.
From http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_05
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Some regions of DNA control other genes, determining when and where other genes are turned "on". Mutations in these parts of the genome can substantially change the way the organism is built. The difference between a mutation to a "control gene" and a mutation to a less powerful gene is a bit like the difference between whispering an instruction to the trumpet player in an orchestra versus whispering it to the orchestra's conductor. The impact of changing the conductor's behavior is much bigger and more coordinated than changing the behavior of an individual orchestra member. Similarly, a mutation in a gene "conductor" can cause a cascade of effects in the behavior of genes under its control.---------------------

Let us know talk about some negative effects

In 1910, Herrick (hope I spelled it right) provides the first description of sickle cell anemia - when he reports that blood smear of a student at Chicago college had pear shaped and elongated forms. Since then several scientists have researched this disease. We now know that this disease is caused by a mutated version of the gene that helps make hemoglobin — a protein that carries oxygen in red blood cells. When red blood cells carrying mutant hemoglobin is deprived of oxygen the red blood cells becomes sickle shaped. These sickle shapes can restrict the flow of blood in the body, causing death. Pittsburgh Steelers (Foot ball team) safety (whose name I do not remember) has sickle cell disease and when he visits Denver Broncos (Denver's foot ball team) he does not play. Due to Denver's elevation ( one mile above sea level) there is less oxygen to go around and this can cause his red blood cells to sickle up. Although he is depressed about not playing, he is doing the smart thing.
Here is another weird fact: Scientists have been studying flies carrying Hox mutations (We will leave Hox mutation alone for now - let us just say it is a type of gene) sprout legs on their foreheads instead of antennae







Now on to some positive effects:

Courtesy:www.tiktaalik.us


Scientist, Neil Shubin has devoted his life to finding the transitional forms. Transitional form is the evolution by which a species transforms itself to a completely different form providing a platform for evolutionary change. (Sort of like conductor gene changes). He started his research on Elsmers island (a remote island near north pole). He set up camps there and started digging through the fossil records. The conditions were harsh - the island was accessible for only a few months of the year. He made 4 trips to the island and was almost giving up on his quest mainly due to high cost of conducting the research. On his last trip, he got lucky - he found a snout of a fish on a rock that was 375 million years old. It was the transitional form he was looking for - The first land fish which had limbs that it used to push itself around - It is now called "Tectalic". it had an arm like fin which is the basic bone structure of every land animal today. Tectalic had evolved to survive from big fishes. Well if it were not for Tectalic we humans would not be here today. Such is the power of evolution - rather mutation.

Mutation is such an important topic and we will revisit this topic through out our Genetic journey blogs.

Saturday, November 12, 2011

Genealogy Data Communication

Genealogy Data Communication

Genealogy Data Communication or GEDCOM is a specification which is used to exchange information between different genealogy software. It is a plain text file of the '.ged' format used for sharing genealogical information of individuals and meta data linking their information records.

The GEDCOM formats are supported by most of the genealogy software available and in use today. This format was developed by the Family History Department of The Church of Jesus Christ of the Latter-Day Saints as a support system for the genealogical research. This file can be read in editors like Notepad or Textpad and hence allows various types of computers and programs to share genealogical data. Its format and usage are described in a written and open specification. The format was readily adopted by different vendors in a variety of software products and has become a standard for genealogy programs. Genealogists, the world over use GEDCOM to save,transfer and edit files containing genealogical data.

The Concept
GEDCOM structure is the collection of data based on a nuclear family and the concerned individual name. It is neither a verification model nor goes deep into research for the 'original' form, if it exists. This format simply allows the structuring of data in accordance with the records of the family and individuals as entered in the storage. Each GEDCOM file contains a header, trailer and a record section. The records section comprises certain notes and the data specification as IND for individual or FAM for family record and so on. Much like an excel sheet, every GEDCOM file contains the top level of the main top-level records like IND, FAM or NOTE. The other level numbers are positive integers incorporating further information on the subject.

It is simply a database of records wherein the pointers track the location of the relation and the individual concerned. For example, a name 'Sara Parker' would be enlisted or found in the file sharing database of the 'Parker' family tree and can be traced with reference to the searched genealogical base. Thus, there are two sections of a GEDCOM file. The first section includes the name and information of an individual. The second section lists all the associated relationships of that individual.

Working with GEDCOM files
Although, a GEDCOM file can be read by any text editor, it is always preferable to use a software application that is specially designed for viewing tree diagrams or GEDCOM formats. The first and foremost step on downloading or on receiving a GEDCOM file through an e-mail account, is to save it in a safe and easy to locate place on the hard drive. Ensure the authenticity of the genealogy file. As stated earlier, the format or the file extension is '.ged'; although, a compressed GEDCOM file uses a '.zip' extension. A file created in a tree diagram format by a random genealogy software program is not the recommended format to be used. Last but not the least, the file has to be decompressed, if at all it is in a zip file and then opened with the existing GEDCOM format. The file systems used in GEDCOM's lately, allow a great deal of flexibility in its usage. Multimedia files capturing your precious events like a marriage or birthday parties can also be stored in this format. The latest version in development is the GEDCOM 6.0, also known as GEDCOM XML.

Until now, the GEDCOM files were limited to the desktops of the genealogists. A new concept called the GenWeb, which means GEDCOM on the Internet allows instant access to a database of any family tree and all the associated services. GEDCOM files save as much as 80% storage space as compared to a '.txt' file format. An usual family tree format with all the graphic features saves a data of 2000 family members in a 6MB file, a GEDCOM format stores the same in 450 K bytes file. Future genealogy programs will integrate reasoning and require proof along with the entry in a database. For example, any significant event will have to be supported with corresponding evidences or reasoning to validate its authenticity.

Let us hope that with GEDCOM, the information becomes more detailed and as trustworthy as possible.
By Prashant Magar