Study in university of UK

Scientists to sequence DNA of cystic fibrosis superbug

Published on 21 Feb 2011

Scientists at the University of Liverpool are using the latest DNA sequencing technology to understand the diversity of a bacterium that causes severe lung infection in cystic fibrosis patients.
The bacterium, called Pseudomonas aeruginosa, is the most common cause of persistent and fatal lung infections in cystic fibrosis patients. Scientists at Liverpool identified a particularly virulent strain of the bacteria that is transmissible between patients. The Liverpool Epidemic Strain (LES), referred to as a cystic fibrosis 'superbug', can cause aggressive infection and results in progressive lung decline.
The team from the University's Institute of Infection and Global Health took samples from patient sputum and cough swabs to understand why the infection is so aggressive in people with cystic fibrosis. They found that during chronic infections the bacteria has the ability to mutate rapidly, resulting in huge diversity. Tests also show that the bacteria produce a molecule that could be the trigger for episodes of acute infection in patients.
Dr Craig Winstanley, member of the National Institute of Health Research (NIHR) Biomedical Research Centre (BRC) at Liverpool, explains: "Patients with LES need to be separated from others in hospitals, so that infection does not spread between cystic fibrosis patients on wards. Once established, these chronic infections can never be cleared. We found that the bacteria have the ability to diversify into hundreds of distinct sub-types, making it very difficult to decide which antibiotic to use for a successful outcome.
"Using the latest DNA technology we have the unique opportunity to study the behaviour of bacteria during chronic infection in real time. This will allow us to get a clearer picture of how it adapts so efficiently to cystic fibrosis patients. If we can understand how and why it behaves the way that it does we may be able to target more effective treatments for the infection."
Working with scientists at the University's Centre for Genomic Research, the team will use new DNA sequencing technology to read the genetic code of the infection. The first of its kind in the UK, the machine works 250,000 times faster than technology used to sequence the human genome 10 years ago.
Dr Steve Paterson, from the University's Institute of Integrative Biology, said: "Each cystic fibrosis patient can be infected with a diverse population of bacteria and it is therefore essential to test samples of the disease from a number of patients in order to understand how it evolves. The technology we are using can read 30 billion letters of DNA sequence per day, compared to four billion using current machines. It will allow us to investigate the mutations of the infection in precise detail, giving us valuable information about the progress of this serious medical condition."
The research is funded by the Wellcome Trust.

Notes to editors:

1. The research follows a University study on Pseudomonas aeruginosa published in the American Journal of Respiratory and Critical Care Medicine. The work, in collaboration with Dr Martin Walshaw from the Liverpool Heart and Chest Hospital, was supported by the Dr Hadwen Trust and the NIHR through the Liverpool Biomedical Research Centre.
2. The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. It supports the brightest minds in biomedical research and the medical humanities. The Trust's breadth of support includes public engagement, education and the application of research to improve health. It is independent of both political and commercial interests.
www.wellcome.ac.uk
3. The NIHR Biomedical Research Centre (BRC) in Liverpool is one of 12 in the country and is funded by the National Institute for Health Research (NIHR) and the North West Development Agency (NWDA). It is run jointly by the University of Liverpool, the Royal Liverpool and Broadgreen University Hospitals Trust and the Liverpool School of Tropical Medicine. The Centre focuses on four areas of microbial disease – hospital and community acquired infections, chest infections, sexual health, and safety of antimicrobial drugs.
4. The NIHR provides the framework through which the research staff and research infrastructure of the NHS in England is positioned, maintained and managed as a national research facility. The NIHR provides the NHS with the support and infrastructure it needs to conduct first class research funded by the Government and its partners alongside high-quality patient care, education and training. Its aim is to support outstanding individuals (both leaders and collaborators), working in world class facilities (both NHS and university) and, conducting leading-edge research focused on the needs of patients. www.nihr.ac.uk
5. The University of Liverpool is a member of the Russell Group of leading research-intensive institutions in the UK. It attracts collaborative and contract research commissions from a wide range of national and international organisations valued at more than £110 million annually.

Fundamentals of Cell and Molecular Biology

• Offered for Year: 2011

• Module Leader(s): Dr Ethan Hack

• Owning School: Biology

Semesters

Semester 1 Credit Value:	10

Aims

To survey the fundamentals of cell and molecular biology and introduce key methods used in research on these subjects. This module is intended for students taking Masters-level courses in biological subjects who have not undertaken degree-level study of cell and molecular biology or who need to refamiliarise themselves with these topics.

Outline Of Syllabus

Introduction: genes and cells.
Proteins: composition and structure.
Organisation of prokaryotic and eukaryotic cells.
Protein synthesis: transcription and translation mechanisms.
Principles of regulation of gene expression.
Genomes: prokaryotic, eukaryotic nuclear, mitochondrial, and plastid.
Essential techniques in molecular biology: DNA cloning, library screening, PCR, detection and measurement of gene expression, DNA sequencing.
Revision Lecture
Lab: fundamentals of recombinant DNA technology.

Teaching Methods

Teaching Activities

Category	Activity	Number	Length	Student Hours	Academic Staff Contact Hours	Comment
Scheduled Learning And Teaching Activities	Lecture	17	1:00	17:00	17:00	N/A
Guided Independent Study	Assessment preparation and completion	17	2:00	34:00	0:00	Exam revision
Guided Independent Study	Assessment preparation and completion	6	1:00	6:00	0:00	N/A
Scheduled Learning And Teaching Activities	Practical	4	6:00	24:00	24:00	N/A
Guided Independent Study	Independent study	19	1:00	19:00	0:00	N/A
Total				100:00	41:00

Teaching Rationale And Relationship

The lectures review background, explain key concepts and outline illustrative examples. The final lecture is a revision session. The in-class test assesses students' progress and provides students with an opportunity to answer practice exam questions. The practicals give students hands-on experience, with supervision and guidance, with recombinant DNA technology and the use of computers to analyse DNA and protein sequences. Private study is necessary for students to absorb information presented in lectures, to deepen their knowledge and understanding through reading supporting material, and to complete the analysis of data from the practicals.

Assessment Methods

Exams

Description	Length	Semester	When Set	Percentage	Comment
Written Examination	90	1	A	70

Other Assessment

Description	Semester	When Set	Percentage	Comment
Practical	1	M	28	To answer structured questions
Other	1	M	2	Exam Practice

Assessment Rationale And Relationship

The exam (choice of 3 from 5 multi-part questions) assesses knowledge and understanding of the relevant subject material and the ability to integrate information from lectures and additional reading. A structured set of questions (deadline week 8) assesses students’ ability to produce, record and interpret data from experiments involving recombinant DNA technology. The exam practice (week 8) assesses students' progress in developing command of the course material and gives students the opportunity and incentive to develop their exam technique.

Reading Lists

• Reading List Website : reading.ncl.ac.uk
• BIO8009's Reading List

DNA study into European ancestry

A team of international researchers led by British experts has challenged evidence over the genetic signature of most European men.
The findings effectively deal a blow to the idea that most are descended from farmers who migrated from the Near East 5,000-10,000 years ago.
Latest research favours the idea that most men in Europe trace their lineage to stone-age hunters though experts acknowledge more work is needed on this suggestion.
The latest study, published in the journal Proceedings of the Royal Society B, focused on the Y chromosome.
More than 100 million European men carry a type called R-M269, which is most common in western Europe, though a Leicester University study from 2010 showed that the genetic diversity of R-M269 increases in the east, peaking in modern Turkey.
This backed a Neolithic origin for the R-M269, though another paper supported a Palaeolithic origin.
In the latest research a team including Cristian Capelli and George Busby at Oxford University have explored the question.
They suggest there are no geographical trends in the diversity of R-M269 and that some of the markers on the Y chromosome are less reliable than others for estimating the ages of genetic lineages.
However, Dr Capelli stressed his study could not answer the question of when the ubiquitous R-M269 expanded in Europe, although his team is carrying out more work on the subject.
Co-author Dr Jim Wilson from the University of Edinburgh explained: “Estimating a date at which an ancestral lineage originated is an interesting application of genetics, but unfortunately it is beset with difficulties.”

Study: DNA is as stretchy as nylon

Researchers at the Institut Laue-Langevin have used neutron scattering to work out how stretchy DNA is, after many previous studies produced very different answers. The results can help to explain how DNA can bend and split in order to establish traits in living organisms and then pass these on from generation to generation.
DNA's characteristic double helix is constantly twisted, bent and stretched when it's inside a cell. How the DNA responds to this pressure is what determines two of its biological functions --replication and transcription.
Previous measurements of DNA stretchiness have varied by an order of magnitude, between 0.3 to 3 newtons per metre. And even these figures are lower than other's produced from sound velocity measurements. The neutron scattering revealed that DNA has a flexibility of 83 newtons per metre -- roughly the same as nylon.
Researchers took wet-spun samples of DNA, which they wound onto a bobbin. These were then placed into a neutron scattering spectrometer. The team measured how the frequency of sound waves running along the double helix structure changed with their wavelength. Professor Mark Johnson, an ILL physicist, explained: "We are essentially measuring the speed of sound in DNA, which gives you a direct measurement of its structural flexibility."
By using computer simulations of the DNA stretching, they could then account for the whole range of previously reported values. They noticed that the solution used to suspend the DNA -- composed of charged ions like lithium and sodium in water to mimic cell conditions -- can influence the stiffness of the DNA. If DNA is pulled sharply, it tends to block -- much like a seatbelt -- because the ions in the solution get between DNA atoms. However if it is pulled slowly it stretches.
The stretchiness that researchers at ILL determined closely supports recent work on the overstretching of DNA. The DNA's structure has been shown to unwind and unzip -- starting the replication process that drives genetic inheritance -- in response to tension inside the cell because the structural stiffness prevents the double-strand DNA molecule from extending.
Dr Lambert van Eijck, one of the lead authors, from Delft University of Technology, The Netherlands: "Our findings support increasing evidence that suggests DNA's stiffness is an important factor in how it is stored in cells and then unzips, starting the replication process that drives genetic inheritance

Why Is DNA Testing Good for Crime?

The average viewer of crime dramas on television or film, as well as the interested fiction and non-fiction reader, will undoubtedly be aware of the benefits of using DNA testing as part of a criminal investigation. While witnesses can lack credibility or fail to recall relevant details, and other circumstantial evidence may be inconclusive, DNA has the potential of identifying the actual perpetrator of a crime with an astonishing level of accuracy. This makes DNA testing not only good for crime, it makes it necessary.

1. History

   • DNA testing, in many ways, has its origins in the 1920s, with the advent of blood-type testing. While blood type is general in nature, testing individuals and comparing it with samples of blood found at the crime scene could help to eliminate certain suspects. This began the trend of using bodily material as a way to identify individuals involved in crimes, an approach that is mirrored to today with DNA testing.
     The first reliable DNA test used to identify individuals became available in 1985 through the research of Sir Alec Jeffreys. Subsequently, it became increasingly used as a tool to identify suspects in criminal cases, beginning with agencies such as the FBI for high profile cases, and eventually moving down to the state and local level for all manner of criminal investigations.
     Further advancements in testing have allowed for more discriminating tests, and ones which allow for the use of very minute or degraded samples, thus allowing scientists to increase the accuracy of identification. In the early days of DNA testing, the samples obtained from hair, saliva, semen, blood and other identifiers needed to be quite fresh in order to match the sample to a specific person. Due to these early problems, DNA was seen as unreliable for use in court as evidence. As better techniques were developed and the science of genetics in general improved, the tests became more reliable and were gradually accepted into the court system. The first case where DNA was admitted into evidence was Andrews v. Florida in 1988.

   Identification of Suspects

   • Obviously, the greatest benefit that comes from DNA testing is the ability to identify who exactly was present at the time of a crime. While characterized as circumstantial evidence (meaning it does not directly prove innocence or guilt), it nonetheless serves as a very powerful tool for both an effective prosecution and defense. To illustrate, let us say that following a rape, the police find witnesses that attest to having seen a particular individual following the victim around the time of the incident. Without any other evidence, this may be insufficient to mount an effective prosecution, especially if for whatever reason the victim can't identity the suspect. With DNA testing, though, one can take whatever samples are available and compare them with that of the suspect. If there is a match, then the case has a much better chance of being successful. If it is not a match, then the suspect can use that to defend against any charges filed. We can thus say that DNA testing is a double-edged sword, useful both to defense attorneys and the state in its efforts to secure convictions.

   Proving Innocence

   • In recent years, much attention has been focused on how DNA testing can exonerate those who have already been convicted of a crime though other evidence. According to Reason Magazine, as of 2008, around 220 people have been exonerated of crimes they did not commit. This includes people who have been in prison for years on charges of murder, rape and other serious violent crimes. Even death row inmates on the brink of execution have been saved at the last minute due to DNA testing of samples that had been sitting in storage for several years. Despite Blackstone's famous line that it is "better that 10 guilty persons escape than that one innocent suffer," our current system sometimes seems to lean on the side of zealous prosecution and high conviction rates, often resulting in innocent people going to jail through misuse of evidence. Some studies have shown that forensic scientists, who are supposed to maintain an impartial attitude when analyzing evidence, have been found to be actively skewing evidence in favor of the prosecution and at the expense of a suspect, according to data collected and analyzed in the book "Forensic Science Under Siege," by Kelly Pyrek. In light of this disturbing reality, impartial DNA testing can help to correct this problem by providing suspects a way to defend themselves when the whole system seems to be against them.

   Limitations

   • While there are many good uses of DNA testing for crimes, there is also the potential for abuse or negligence. For example, if there is more than one DNA sample at a crime scene, it can be difficult to determine what, if any, relationship a person has to a crime. If there are other samples around from other sources, then the situation becomes very complex and DNA testing can become inconclusive in determining guilt or innocence.
     Also, there have been cases where DNA tests have been tainted through contact with other samples, and where the results of tests were misstated or mis-characterized in court. It is clear then that DNA testing is merely one more tool available to enhance the pursuit of justice and by no means the Sine qua non of criminal investigation.

   Concerns

   • There is a growing call to establish a national DNA database to augment the one currently maintained by the FBI on convicted criminals. Some call on everyone, regardless of their criminal history, to be included. Others, seeking a less controversial approach, seek to obtain DNA samples from anyone arrested or questioned in relation to a crime. These measures bring up important concerns for privacy and the presumption of innocence enshrined within our legal institutions. Investigations into high profile crimes, for example, have already been used to ask otherwise innocent people to "volunteer" their DNA in order to be eliminated as a potential suspect. This entails citizens having to prove their innocence as opposed to the state having to prove guilt beyond a reasonable doubt. Therefore, like all technological advancements, DNA testing has the potential for negatively altering our society in ways that outweigh the benefits that it provides.

 

Why Is DNA Testing Good?

DNA, or deoxyribonucleic acid, is a chemical involved in the storage of genetic information. DNA tests are a very specific method of identifying an individual. This is useful in criminal cases as DNA evidence is often used to free prisoners who have been wrongfully convicted of committing crimes. DNA tests also provide genealogical information, which can help a person learn who their ancestors are. DNA testing also allows a person to know about diseases they are at risk for, so they can modify their lifestyle to reduce the chance of getting sick.

1. Immigration

   • The United States immigration process asks immigrants if they have other relatives living in the United States. Immigrants to the United States do not always have legal documents proving that they have a biological relationship to United States citizens. The State Department allows immigrants to submit DNA samples which are used to prove that an immigrant is related to current United States citizens when the immigrant does not have other legal documents necessary to prove their relationship.

   Paternity

   • DNA testing also provides evidence of paternity. The government can require child support payments to make a father support his children if DNA proves he is the father. A man can also use DNA test results to prove that he is not the father of a child, to contest a child support obligation.

   Disasters

   • DNA testing identifies the victims of natural disasters and military attacks. Bodies are not always found in recognizable condition, especially if some time passes. A DNA test does not need a large amount of material to clearly identify an individual. After the World Trade Center attack, DNA testing was very useful in identifying the victims, according to the President's DNA Initiative.

   Criminal Justice

   • Some people are convicted of crimes they did not commit. The National Institute of Justice issued a report that named 28 prisoners who were exonerated by DNA evidence. DNA evidence can also be used to convict a defendant of a crime. According to the National Criminal Justice Reference Center, DNA evidence was first produced as courtroom evidence in 1986, and is now valid evidence throughout all jurisdictions of the United States.

   Diseases

   • Genetic testing helps people screen for diseases. A DNA test can show whether two people are at risk for passing diseases to their future children. DNA testing can detect genetic disorders in a fetus. According to the National Institutes of Health, DNA tests can detect a genetic disorders before a person suffers noticeable disease symptoms, as well as confirming a physician's diagnosis of a genetic disorder.

Tougher controls sought for DNA ancestry testing

BERKELEY — As the popularity of take-home DNA kits to trace ancestry or calculate the risk for serious medical conditions grows, there is an increasingly critical need for federal oversight of "direct-to consumer" genetic testing, as well as of the use of DNA samples for research, according to researchers from the University of California, Berkeley, and several other academic institutions.
In the past year, scientists, sociologists and bioethicists, among others, have come to agree that the technology of these direct-to-consumer tests, which run between $100 and $1,000 apiece, is problematic and that the test results can be misleading and lead to problems including skewed ethnic data and questionable membership claims to Native American tribes.
But while organizations such as the American Society of Human Genetics have issued guidelines to curb the unintended consequences and misuses of DNA testing, federal agencies need to step in and help shape a "gold standard" in genetic ancestry testing, according to a policy paper published in the July 3 issue of the journal Science and coauthored by researchers from UC Berkeley, Stanford University, the University of Texas, University of Wisconsin and New York University.
"We encourage regulatory agencies such as the Federal Trade Commission, the Food and Drug Administration, and the Centers for Disease Control to help set industry standards for responsible and accountable practices in genetic ancestry testing," said coauthor Kimberly TallBear, assistant professor of science, technology and environmental policy at UC Berkeley.
The article in Science is a direct response to the American Society of Human Genetics guidelines, which recommend increased accountability, transparency and collaboration among consumers, scientists and the companies selling take-home genetic ancestry kits.
"We take the position that overcoming the most difficult ethical challenges of genetic ancestry testing will depend on the political will of federal agencies to prioritize values of transparency, responsibility and communication," said Sandra Soo-Jin Lee, a medical anthropologist at the Center for Biomedical Ethics at Stanford University and lead author of the policy paper.
Lee and other authors argue that voluntary collaboration and transparency are unlikely to succeed because of the proprietary nature of companies' and institutions' genetic databases; the power disparity between scientists and their research subjects; and the diverse and possibly conflicting interests of stakeholders who don't even share a common language. For example, TallBear said, "Whose definition of 'origin' will prevail?"
"To a geneticist, origin might refer to ancestral populations inferred for an individual on the basis of specific genetic markers, specific algorithms for assessing genetic similarity and specific reference populations," the article says. "To a casual consumer, 'origin' might mean 'the country where I was born' ... to a Native American, origin might also signify the landscape feature or event where his/her people emerged or acquired their identity."
According to news reports, a half million consumers have purchased genetic ancestry tests, which are sold by more than two dozen personal genomics companies with names such as "Roots for Real," "23andMe" and "DNA Tribes." Typically, the test taker swipes the saliva inside his or her cheek and sends the swab to the lab. The DNA is extracted and compared to samples from a reference database of haplotypes (sets of inherited, linked genetic markers) to see if there's a match.
Different tests use different methods. For example, mitochondrial DNA tests trace the mother's lineage, while Y-chromosome tests track paternal ancestry. But because these tests only trace one bloodline, they exclude most ancestors. Moreover, they cannot pinpoint where these ancestors lived.
Another option is AncestryByDNA, a genealogy test that relies on markers that show genetic differences between what are assumed to be four biologically distinct populations: Africans, Europeans, East Asians and Native Americans. But some groups that don't fit neatly into these categories, such as South Asians and Middle Easterners, have received test results identifying them as Native Americans, for example, according to researchers.
Also critical to resolve, according to the article, are the ethical issues concerning the collection and use of DNA samples. For example, members of the Havasupai Tribe in Arizona allege that researchers from Arizona State University and the University of Arizona collected 400 blood samples from tribal members for diabetes research. But, according to news reports, those same samples were also used for unauthorized research on schizophrenia, inbreeding, and population migration, which stigmatize tribe members. The Arizona Court of Appeals ruled late last year that the Havasupai tribe can sue the Arizona Board of Regents, which is seeking to settle the case.
"It is a scientific imperative that we enact enforceable policies that determine what constitutes responsible and accountable collection and secondary use of DNA samples," the article says.
In addition to Lee and TallBear, coauthors of the article are Troy Duster, professor of sociology at UC Berkeley and New York University; Deborah Bolnick, assistant professor of anthropology at the University of Texas; and Pilar Ossorio, associate professor of law and bioethics at the University of Wisconsin Law School.

DNA Ancestor Testing

 

DNA testing has become an increasingly popular method of determining ancestry, but a set of standards for these tests has yet to be codified. Generic DNA tests result in ancestral data that is not 100% complete.

1. How It Works

   • DNA tests to determine ancestry are commonly available for anywhere from $100 to $1,000. A swab from the inside of the mouth is sent to the testing facility, where several methods may be employed to run the test. For example, Y-chromosome tests help determine paternal ancestry, while mitochondrial tests determine ancestry on the mother's side.

   Issues

   • DNA tests for ancestry are limited. Since each test looks at only one bloodline, many ancestors are left out, and the individual being tested will be left with many unanswered questions. There is also no way of telling from DNA where ancestors actually lived. Results may vary from test to test, depending on the method used to collect data, and it is nearly impossible to interpret the results objectively, given the variance.

   The Future

   • As the process is developed over time, many issues regarding DNA ancestry testing may be effectively resolved. More detailed tests may be developed, and the significance of certain ancestral populations on modern day people may be better defined. Scientists are working to develop standards that will lead to better methods of interpreting results.

Technology Required for DNA Testing

The technology used in DNA testing involves scanning 13 specific regions of DNA. There is only a very small possibility that, once the scan is complete and the DNA identified, the DNA could belong to another person. This DNA testing, or scanning, can be done utilizing five different technologies.

1. Functions

   • DNA testing can be done to match evidence with possible criminals, and victims, at crime scenes. This testing can also rule out crime suspects. On a personal level, DNA testing can determine a child's paternity and even match organ donors to potential recipients.

   Features

   • DNA testing is done by exposing genetic material to enzymes and charting the result, scanning and analyzing specific DNA sequences, extracting specific proteins from DNA, and analyzing genetic markers to determine such things as paternity.

   Considerations

   • Forensic scientists have applied all the various technologies to test DNA to smaller and smaller samples of genetic material. At the inception of DNA testing, some tests required the use of genetic material at least the size of a U.S. quarter dollar. Now DNA testing can even be tried when biological evidence is sparse.

 

DNA Parentage Testing

DNA Samples

• Samples for DNA testing can be taken from the inside of the mouth using a swab. This method of collecting cells is known as a buccal swab, and is painless and easy. Blood samples can also be used for DNA tests.

Paternity and Maternity

• Paternity tests are used to determine the father of a child. In paternity tests, the child's DNA is studied and compared to its mother's genetic characteristics. The genetic traits that are the same as the ones found in the mother are then excluded and the remaining characteristics are assumed to from the biological father. In the event the man being tested has DNA that includes these remaining genetic characteristics, then the chances that he is the father can be determined. However, if the man being tested has DNA that does not match these remaining genetic characteristics, it can be concluded that he is not the father. In the maternity testing process, samples from the mother and child are necessary, and may also use DNA samples from the father.

Accuracy

• Advances in genetic testing have led to DNA tests that are 99.5 percent accurate. There is no difference in accuracy between a DNA test using a blood sample or a test using a cheek swab.