(Press-News.org) As genome sequencing has gotten faster and cheaper, the pace of whole-genome sequencing has accelerated, dramatically increasing the number of genomes deposited in public archives. Although these genomes are a valuable resource, problems can arise when researchers misapply computational methods to assemble them, or accidentally introduce unnoticed contaminations during sequencing.
The first complete bacterial genome, Haemophilus influenzae, appeared in 1995, and today the public GenBank database contains over 27,000 prokaryotic and 1,600 eukaryotic genomes. The vast majority of these are draft genomes that contain gaps in their sequences, and researchers often use these draft sequences for future analyses.
Each genome sequencing project begins with a DNA source, which varies depending on the species. For animals, blood is a common source, while for smaller organisms such as insects the entire organism or a population of organisms may be required to yield enough DNA for sequencing. Throughout the process of DNA isolation and sequencing, contamination remains a possibility. Computational filters applied to the raw sequencing reads are usually effective at removing common laboratory contaminants such as E. coli, but other contaminants may be more difficult to identify.
In a new study in PeerJ , authors from Johns Hopkins University discovered contaminating bacterial and viral sequences in "draft" assemblies of animal and plant genomes that had been deposited in GenBank. These may cause particular problems for the rapidly growing field of microbiome analysis, when sequences labeled as animal in origin actually turn out to be microbial.
In an even more surprising finding, the authors discovered the presence of cow and sheep DNA in the supposedly finished genome of a pathogenic bacterium, Neisseria gonorrhoeae. Although deposited in GenBank as a finished genome, the bacterium apparently was a draft genome that was submitted as complete, with erroneous DNA inserted in five places. If taken at face value, this data would appear to be a startling case of lateral gene transfer, but the correct explanation appears to be more mundane.
These findings highlight the importance of careful screening of DNA sequence data both at the time of release and, in some cases, for many years after publication.
INFORMATION:
The landmark discovery of a tiny defect in a vital heart protein has for the first time enabled heart specialists to accurately pinpoint a therapeutic target for future efforts in developing a drug-based cure for cardiovascular diseases.
Scientists from Cardiff University and the Slovak Academy of Science have identified defects in a colossal heart protein which often leads to stroke and heart failure.
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Ultimately, the team say their work may help researchers understand more about normal brain function and about neurocognitive disorders such as dementia.
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Inhibitory neurons ...
CHARLOTTESVILLE, VA (NOVEMBER 18, 2014). Neurosurgeons and neurointerventionalists at Kyungpook National University in the Republic of Korea have developed a formal protocol for delivering emergency treatment to patients with subarachnoid hemorrhage (SAH) from ruptured aneurysms within the first few hours after bleeding occurs. The emergency treatment plan, offered day and night, is shown to reduce the incidence of repeated hemorrhage during the hospital stay and improve clinical outcomes in patients with aneurysmal SAH. This treatment plan is described and discussed in ...
OAK BROOK, Ill. - Radiologists from the National Institutes of Health (NIH) and Emory University School of Medicine have issued a special report on radiology preparedness for handling cases of Ebola virus. The report, outlining their protocols and recommendations, is published in the online edition of the journal Radiology.
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New federal regulations requiring school meals to contain more whole grains, less saturated fat and more fruits and vegetables, while perhaps improving some aspects of the food being served at schools across the United States, may also be perpetuating eating habits linked to obesity, diabetes and other diet-related diseases, an analysis by Johns Hopkins Bloomberg School of Public Health researchers has found.
The reasons: Based on analysis of school meals and the new requirements, the whole grains served are mostly processed, which means they are converted into sugar ...
NEW ORLEANS (Nov. 18, 2014) - Researchers from Drexel University in Philadelphia will present research on a wide range of public health topics emphasizing urban health challenges, geographic methods in public health, community resilience and more, at the 142nd annual meeting and exposition of the American Public Health Association Nov. 15-19.
A few selected highlights among the dozens of posters and presentations by faculty, staff and students from the Drexel University School of Public Health include:
What Makes Communities Resilient in Times of Adversity?
Psychologists ...
Early sodium supplementation for very premature infants can enhance weight gain according to a recent study by researchers at the University of Cincinnati Medical Center and Cincinnati Children's Hospital Medical Center.
The results of the study, published today in the OnlineFirst version of the Journal of Parenteral and Enteral Nutrition (JPEN), the research journal of the American Society for Parenteral and Enteral Nutrition (A.S.P.E.N.), examined 53 infants during the first months of life who had been born at less than 32 weeks of pregnancy.
Poor growth of premature ...
Researchers at Indiana University-Purdue University Indianapolis say acculturative stress may explain, in part, why Indiana's Latino youth face an alarming disparity in depression and suicide rates when compared to their white counterparts.
While examining epidemiological health disparities data, a team of researchers led by Silvia Bigatti at the Richard M. Fairbanks School of Public Health noticed that Latino teens in Indiana had a 65 percent higher rate of suicide attempts and a 24 percent higher rate of depression than white teens.
"When we saw the alarming disparity ...
Promoting and maintaining financial fraud whistleblower programs, such as those of the Securities and Exchange Commission (SEC) and the Commodity Futures Trading Commission (CFTC), is costly.
Cases involving whistleblowers require significant resources as they take nearly 10 months longer to complete. Rewards for whistleblowers who come forward with original information leading to an enforcement action can be large, ranging from 10% to 30% of monetary sanctions over $1 million. This past September, the SEC awarded $30 million to a whistleblower--it's largest award yet. ...
Researchers are studying the Caulobacter crescentus bacterium because of its developmental process and cellular cycle, which serve as models for a number of pathogenic bacteria. They all have in common the use of polysaccharides to create a particularly effective protective envelope, or capsule. Professor Viollier's laboratory at the University of Geneva's (UNIGE) Faculty of Medicine has just unraveled the secrets of capsule formation during the cellular cycle and perhaps even identified potential Achilles' heel of bacteria. These results were published in the last edition ...
