“We began this project because we needed more reliable methods to do our own research work, which involves detecting resistance genes and other genetic markers in thousands of bacterial genomes, but we quickly saw that it had direct and important implications for diagnostic labs.”
In this Q&A, Michael Inouye and Kathryn Holt, authors of a Software article recently published in Genome Medicine, tell us about the development of the software SRST2. SRST2 is a read mapping-based computational tool that allows fast and accurate detection of genes, alleles and multi-locus sequence types from whole genome short sequencing reads.
Why did SRST2 need to be developed?
“Genomic surveillance is being adopted by diagnostic and public health labs all over the world, as …
Can health economics and the practical realities of delivering healthcare work side by side? Michel Wensing, professor of implementation science at Radboud University Medical Centre, Nijmegen, Netherlands, and co-editor-in-chief of Implementation Science considers a new editorial on this question.
Many health professionals and health researchers have little interest in the costs of healthcare, perhaps with the exception of their personal reimbursement. Published economic studies have little relevance for them.
And, in fact, they may be correct. Economic analyses in healthcare are often designed to support decision-making on the reimbursement of treatments, devices and programs in national healthcare systems. Therefore a societal perspective and long-term time horizon are taken, non-healthcare costs are included, and non-clinical utilities are preferred …
This is a guest blog by Steve Commins from Thematic Working Group on Health Systems in Fragile and Conflict-Affected States.
Despite fifteen years of donor efforts to define and address fragile and conflict affected states, the global aid system remains inconsistent in its approach to situations of conflict – veering from rapid (and solely) humanitarian, short term responses, to more nuanced investments in longer term tactics and support for health systems. A new set of papers provides evidence on the particularities of local fragility and the innovative ways that health systems can be strengthened even in settings in crisis.
The papers in a special issue for, Conflict and Health, provide new reference points to literature on health in fragile …
After watching CSI, and with forensic science being more advanced than ever, it’s easy to presume that criminals leave DNA traces everywhere that can help to make a conviction if they are caught.
Human hairs come to mind as a great place to start, however, the majority of samples recovered at crime scenes are shed hairs containing insufficient levels of nuclear DNA, meaning they cannot be used to make an identification. This is because short tandem repeat (STR) analysis is performed on crime-scene DNA, where probes are attached to the sample, then it is amplified in length by a polymerase chain reaction (PCR) to create a DNA fingerprint. Two samples can then be compared to find if there’s a match. With …
Cheng Cheng is from the School of Life Science & Technology at Xi’an Jiaotong University, China, and Jun Yu is from the Beijing Institute of Genomics, Chinese Academy of Sciences. They are authors of an article published in Genome Biology which has revealed the genomic ‘signatures’ of extinction events in birds. In this post they talk about how these new insights could be used to help conservation efforts of the endangered Crested Ibis in China, and prevent the extinction of other species.
Birds play important roles in ecological balance. They are found everywhere around the globe, with their species numbering nearly twice that of mammals. Unfortunately, the rate of their extinction appears to have increased in the past millennium. …
Research published today in BMC Public Health by Jamie Oliver’s back–to-basics home cooking skills program (Jamie’s Ministry of Food), shows that participants who completed a 10 week-cooking course, increased their vegetable consumption and cooking confidence, as well as changed their cooking and eating behaviors. In this guest blog, Alicia Peardon, CEO of The Good Foundation and Jamie’s Ministry of Food Australia, talks about the merits of the program and how Australians can take steps towards combating diet-related disease.
The Good Foundation is a not-for-profit established in 2010 to focus on programs that promote good health and nutrition, with our first priority being Jamie’s Ministry of Food Australia. We partnered with Jamie Oliver and The Good Guys to …
Today’s guest blog is a Cancer Research UK Career Development Fellow, Jurre Kamphorst, a researcher focusing on the metabolic stress responses in cancer cells and lead author of a study published in Cancer & Metabolism.
Unlike normal cells, cancer cells are wired to just keep on growing. This continued growth requires a constant supply of cellular building blocks, including fatty acids for cell membranes. Normally, fatty acids are mostly being made from glucose. However, tumors often face reduced oxygen levels (hypoxia), causing glucose to be only partially metabolized and secreted as lactate, instead of being used for fatty acid synthesis. We discovered that acetate substitutes for glucose as a source for fatty acid synthesis in hypoxic cancer cells.
We were initially …
New research published today in Clinical Epigenetics questions the methods used in some studies for assessing DNA methylation in cancer, calling for the use of only quantitative techniques. This is a guest blog by Dr Annette Lim (Peter MacCallum Cancer Center, Australia) and Dr Alexander Dobrovic (Ludwig Institute for Cancer Research and Olivia Newton-John Cancer Research Institute, Australia) to explain more about the importance of how we measure DNA methylation in cancer.
Given the critical role of methylation in embryogenesis, it is not difficult to expect that dysregulation of methylation will be a fundamental element in the evolution of uncontrolled cell cycling within the cancer genome. As such, the identification of altered methylation in tumours has held promise of unlocking …
Electronic cigarettes (e-cigarettes, ECs) are the centre of much controversy due to public health concerns associated with some of its components including nicotine which is highly addictive. Additionally, the availability of such devices to young never-smokers and the re-normalization of smoking is a growing concern. This has been highlighted in the news lately where a study shows three times as many children have tried e-cigarettes than those who have smoked tobacco. However, on the other hand ECs are considered to be potentially less harmful than tobacco smoke and are used to aid smoking cessation.
The debate on ECs between clinicians and public health professionals has been discussed extensively at several meetings including the European Respiratory Society,
Nearly 20 years into full genome sequencing, today the cost of sequencing a single genome, once a feat of only the well-funded, is ceasing to be a matter of discussion. Sequencing is merely data gathering for the biology. With this change, journals too have changed. Looking to publish scientific breakthroughs, many journals have stopped considering the sequencing of a whole genome a scientific advancement, or work worthy of publication. But as the cost of sequencing drops, the amount of data in public databases rapidly accumulates. And as with all big data, its great potential lies in its size. We need to be able to view genomes in comparison. Yet there is no contextualisation for this data: what methods were …