DNA Nucleotides

DNA nucleotides are the small repeating units that, joined together by the millions into a long spiral ladder shape, form the DNA strand, also called a DNA molecule or double helix or, simply, DNA. But what exactly are DNA nucleotides and why are they important to DNA sequencing?
Each nucleotide segment in a DNA strand is actually a pair of nucleotides, but is commonly called, collectively, a nucleotide, for ease of use. I'll describe this breakdown visually again so you can see a clear picture: if you take a DNA strand and cut it crosswise so that you now have one rung' with a short section of pole on either side, you'll have a single unit that looks like a capital 'H'; each of those side poles is a short section of what is called the DNA Backbone, and the horizontal rung joining them in the middle is called a Base. We'll separate and discuss the backbones and the bases on the next two pages.
First, this single H shape, though generally called a nucleotide, is actually a PAIR of nucleotides, joined in the middle. If you take that H shape and cut the rung (base) in the middle, you are now left with two pieces, each looking like a capital T turned on its side. NOW you have a single nucleotide. Let's take that single DNA nucleotide and zoom in for yet a closer look.
That single piece of DNA nucleotide is made up of two parts. For visual clarity let's keep looking at it as a sideways T, with the vertical bar being a part of backbone and the horizontal part being the base, the half-rung of the ladder. That's all we need to cover for this page; remember, I'm taking you smaller and smaller, we've cut it down like this so far: the long strand of DNA you see in pictures is shaped as a double helix, actually two long helixes joined down the middle by their half-rungs; if you take that double helix and cut out a single section of it, with one rung and a short section of each backbone, you have a section of the DNA strand known as a nucleotide in general language, and it looks like a capital H. Technically you slice that H in half so it now looks like two capital T's turned sideways. Each of these T's is called, correctly, a single nucleotide.
Now we take a nucleotide and take it apart: we take the half-rung of the ladder, called a base, apart from the side if the ladder, the backbone. Just a few words on each, in the next two pages.

DNA Sequencing

DNA sequencing is any process used to map out the sequence of the nucleotides that comprise a strand of DNA. This website is meant as a primer to show you, step by step, what parts of DNA are being 'sequenced' and why it is such a valuable process for humankind to learn. To do this, I need to give you a linear overview of DNA, starting with how the familiar double-helix DNA strand is structured. When you understand the components of that structure, you understand what DNA sequencing is trying to read.
This works best if read in order; if you start with the 'DNA' page and work yourself down, by the time you arrive at the DNA Sequencing page you should have a pretty clear layman's picture of the constituent parts of DNA and what the parts are that are being sequenced. It is meant to give you a clear but layman's understanding of DNA and DNA sequencing, after which you can look into more technical resources elsewhere if you like.
DNA sequencing is a newer technology; it has been known since the invention of the microscope that some central part of the human cell (and animal and plant cells, any cell of a living organism) has as its core some small piece of information-holding matter that probably contains the blueprint of how each cell in your body is formed. In 1944 DeoxyriboNucleic Acid was discovered to be the chemical comprising this tiny central encyclopedia found in every cell, and the shortening to DNA became a household word.
The evolution of our discovering how DNA is put together has been the greatest contribution to our knowledge of ourselves physically. Scientists have invented and discovered increasingly revealing methods of opening the secrets of DNA; after the discovery of the double-helix shape of DNA in 1953 (see the DNA Sequencing page further down), and seeing how DNA is comprised of a series of ladderlike units known as DNA nucleotides, the primary goal has been to find out just how the sequence of those little nucleotides leads to whether you have blonde or red hair, whether you have light or dark skin, and every other detail from your bone marrow to the tips of your hair; DNA sequencing is seen as the looking glass into the origins of what makes every part of you, large and small, what it is. And DNA sequencing is the prime process by which scientists unravel genetics, the study of how we are put together and how we transfer our traits to our offspring.
If finding DNA was the discovery of the exact subtance holding our genetic makeup information, DNA sequencing is the discovery of the process that will allow us to READ that information. Let's begin with DNA and carry through to DNA sequencing and its uses.

Karachi gang rape shocks Karachiites

Karachi gang rape shocks Karachiites

It took the gang rape survivor less than 24 hours to realise that she was better off withdrawing her statement, so badly did the government and police manage the case.

Twenty-something K and her acquaintance S, in her mid-30s, were driving in a blue Suzuki Alto on Khayaban-e-Qasim in DHA  when three to four men in a car rammed into them from the back. The small car dived into a ditch, the women were dragged from the car, abducted and K was gang raped while S was beaten. They were then dumped back at the spot. M, one of K’s friends, took them to hospital from where the case was taken up.

DIG South Iqbal Mehmood confirmed that the medico-legal report stated that rape had indeed taken place. “The report has been reserved for now and will only be released on Tuesday,” he said. S was beaten and needed 17 stitches, added Citizens-Police Liaison Committee chief Ahmed Chinoy. He told The Express Tribune, “Since there was no medico-legal officer (MLO) at Jinnah hospital they were then taken to Services hospital where the MLO examined the girl and also took samples for DNA testing. The initial report does say that she was raped.” Police Surgeon Dr Hamid Parhiyar said K’s clothes have been handed over to the police. DNA samples have been dispatched as well. Dr Sumayan, who carried out the chemical examination, has declined to comment.

K’s friend M registered the First Information Report (FIR) No. 585/10 under Sections 365-A (kidnapping) and 375/34 (gang rape) of the Pakistan Penal Code at Darakshan police station. It states that there were three to four unidentified men who committed the crime. The complaint was, however, withdrawn late Monday night.

At the Darakhshan police station, where the statements were recorded, a veritable media circus had broken out. Not one to be left out, information adviser Sharmila Farooqui arrived and after attempting to speak to K, met the media at about 7:30 pm. Against all internationally adopted procedures, the adviser not only named the rape survivor but went on to express scepticism and describe K as extremely “hyper” and “rude” as she did not want to speak to anyone. “She’ll beat you with a stick if you go meet her!” Farooqui exclaimed.

The adviser told the media that K had said that she would think about giving names and addresses after mulling over them through the night. Amid a rash of questions, Farooqui discussed M’s statement that led to the FIR. M’s statement was automatically assumed to be K’s version of the events, that she went to a “party” and was raped after she emerged from it. “But this is her version,” said Farooqui. She went on to make the judgement that K’s statements had been “contradictory” because her friends had given different statements and locations.

“You will understand it later [after investigations are through],” Farooqui answered to further badgering from the media. “We’ve understood it a little… Uss [her statements] mein jaan nahi he. Thora sa he.”

Farooqui said that K was blaming the police and politicians for inviting the media. “A perfectly normal person would panic with so much media around,” the adviser admitted.

K was not willing to share details of where she lived, the address of the supposed party she had attended and other information. S was also not keen on divulging any details.

Adviser Farooqui and the CPLC’s Chinoy went on to stress that the rumours of a gang operating in DHA were not true. “There is no such thing. It is an individual, isolated case,” Farooqui said. She expressed sympathy for the police. “The bechara DIG has been sitting here for four hours,” she remarked.

Chinoy, who also spoke to K, said, “She was calm. However given the amount of media present, given what happened, she was disturbed and said that she had not been treated fairly [mere sath insaaf nahi hua he].”

While officials admitted that the medico-legal report showed that K had been raped, the prevailing consensus at the police station was that the women were at fault and were ‘blackmailing’ someone by filing the FIR. When asked about K’s profession, DIG Iqbal Mehmood huffily replied, “She says she is a model.” He then went on to disclose personal biological details about her.

At the police station, there appeared to be an effort to portray that the alleged victims were ‘call girls’ and one of them was involved in ‘trafficking women’. Much was made of the “fact” that the women had reportedly attended a party and that one of their statements did not match.

“The victim is not ready to inform the police about the culprits and she is not even answering when the police ask her from where she was returning home at midnight,” said SHO Rana Amjad. “We did not register the case on the complaint of the victim but we lodged the FIR over media pressure.” The women had not spoken to any media personnel and had left the police station while reporters were amassed outside.

The small car, which had been hit by the alleged perpetrators’ car, stood in the parking lot at the police station. Its front and rear ends had received extensive damage and the windshield was smashed.

Speaking to The Express Tribune on the condition of anonymity, a female police surgeon with 15 years of experience, who works with rape survivors admitted at Jinnah hospital, Civil hospital and Abbasi Shaheed Hospital, said: “We keep asking the (alleged) victim questions and slowly take them into confidence in order to get the whole story. Every now and then we revert to the same questions in order to check for continuity… In some cases the woman may be severely traumatised and when questioned by the police may succumb to pressure.” Dr Mubarak Ali, a medico-legal officer at Civil hospital, also said a victim’s story changes if they get scared of the police.

PPI reported, however, that both women came to the police station on Monday at about midnight and informed the police about the case.

According to this report, the police took them to Civil Hospital Karachi (CHK) for medico-legal formalities. CHK MLO Dr Qarrar told PPI that the initial report suggested that the woman was raped.

Clifton SP Tariq Dharejo told The Express Tribune that the DIG was forming a special investigation team to investigate the matter. The mobile phone records are being pulled as well.

with additional input by mahnoor sherazee

Published in The Express Tribune, December 21st, 2010.

Chain of Custody

We adhere strictly to chain-of-custody regulations. These steps/procedures assure that the correct individual is, in fact, the person from whom the sample derived (in order to avoid possible fraud). We collect samples from persons all over the US and all over the world, even when involved parties may be located in separate cities/countries. Bio-Synthesis' network of trained and qualified doctors, nurses, and phlebotomists all over the US and the world have been trained to perform buccal swab collections (or blood) following our protocols that ensure that strict chain of custody has been kept during each sample collection.
At the time of sample collection, each patient must provide proof of identity. All adults (over 18 years of age) must show a government-issued photo ID (e.g. driver's license, passport, green card);. Additionally, other legal identification may also be required (e.g., social security card, insurance card, birth certificate).
For minors (under 18 years of age), it is sufficient to present a birth certificate and/or a health card and their legal guardians must be present. A photocopy of the presented ID will be made, and a photograph will be taken
(the picture is signed, dated and kept with the person's file). Furthermore, a right thumbprint (or a right footprint from infants) is obtained;. Once all the paperwork is completed, the samples are sealed in the presence of the patient and sent via express courier service directly to our headquarters.
Once the samples arrive in our facilities, they are recorded in our logbooks and, following a thorough inspection of the package, to ensure that the envelope was not tampered with, a case number is assigned and the samples go to the lab, for immediate and proper processing.