News
How a bacteria-detecting strip of plastic film could make best-before dates irrelevant
It's impossible to tell if meat is contaminated with potentially deadly E. coli bacteria by simply smelling or looking at it, but one day a glance at the plastic packaging could let consumers know if it's safe to eat.
That's the hope of a team of researchers at McMaster University in Hamilton, Ont. They've developed a thin, plastic patch they call Sentinel Wrap that changes colour under ultraviolet light when it comes into contact with meat contaminated with E. coli, a food-borne bacteria that can cause extreme illness or death.
Team member Carlos Filipe, chair of McMaster's chemical engineering department, hopes that shoppers will one day be able to point their smartphone cameras at packaged fresh food and check for contamination by using an app. "The goal is to allow people to ultimately look at the packaged food and be able to tell if there is food contamination, like E. coli, in that food, without having to open the package," says Filipe.
The researchers published their findings in April in the scientific journal ACS Nano, but they still have obstacles to overcome before they can test the patch in the real world. It would first need approval from food regulators, then the researchers would have to bring down the cost of mass production.
"We are hoping that in two years' time, with the industry partners that we are currently talking to, we can at least start some pilot studies on these so that we can have some selected food in grocery stores that we can follow and see what happens," says Tohid Didar, an assistant professor in McMaster's chemical and mechanical engineering department. "That's the goal."
In a Rare Genetic Syndrome, a 11-Year-Old Girl Got Most of Her Genes from Father & Almost None from Mother
In a rare case, an 11-year-old girl from the Czech Republic was born with genes that came almost entirely from her father, instead of half from each parent. Only about 25 people in the world – all girls – have been reported with this genetic syndrome and the Czech girl appears to be the first to have inherited it without developing cancer.
Clinical geneticist Jennifer Kalish of the Children’s Hospital of Philadelphia, who was not involved in the new case, told BuzzFeed News, “Ten to fifteen years ago, we didn’t think this condition was compatible for life. It doesn’t happen every day.” Kalish heads a lab investigating ways to help children with imprinted gene disorders, conditions in which at least one gene is doubled up from mom or dad. Although rare, more of these cases are turning up due to improved genetic testing worldwide.
Researchers found the Czech case because the girl’s parents were trying to understand why she was deaf, as reported in April in the Journal of Human Genetics. At nine years of age, a genetic test revealed that she had two identical copies of a rare gene twice, once from each parent. The rare gene was surprisingly not in her mother, wrote the scientific team, led by Irena Borgulova of the Centre for Medical Genetics and Reproductive Medicine Gennet in Prague. It meant she had inherited two copies of her father’s gene. Subsequently testing showed that it wasn’t just that one gene – she had doubled up on her father’s genes in almost all her chromosomes in most of her cells. Only about 7% of her blood cells, for example, showed any maternal genes and 74% of the cells in her saliva held only paternal genes.
How does this happen? In the girl’s case, instead of the DNA from her father’s sperm and mother’s egg pairing up this way, two copies of the father’s genes zipped together to create a dad-dad set of 23 chromosomes, the full human genome. When the zygote split to create more cells, most ended up with the dad-dad genome.
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Hematology
Screening Tool Could Predict Risk of Developing AML Years Before Disease Onset
The incidence of acute myeloid leukemia (AML) increases as people age, but the disease can often appear suddenly in patients, without any detectable early symptoms. However, new research has identified the origins of AML, which can be detectable more than 5 years before the disease develops.
The results, published in Nature, found that blood tests can reveal the roots of AML in healthy patients by looking for changes in DNA code. “We have been able to identify people in the general population who have traces of mutations in their blood that represent the first steps in how normal blood cells begin on a pathway of becoming increasingly abnormal and puts them at risk of progressing to AML,” co-principal investigator John Dick, PhD, FRS, senior scientist at Princess Margaret Cancer Centre, University Health Network, said in a statement. “We can find these traces up to 10 years before AML actually develops. This long-time window gives us the first opportunity to think about how to prevent AML.”
The researchers used data from a large European population health and lifestyle study that tracked 550,000 people over 20 years. The team used data from more than 100 participants who developed AML 6 to 10 years after joining the study, plus data from an age-matched cohort of more than 400 people who did not develop AML. They found that years before an individual was diagnosed with AML, the blood system started to pick up mutations, which allowed the team to predict who had been at risk of disease progression.
“Our study provides, for the first time, evidence that we can identify people at risk of developing AML many years before they actually develop this life-threatening disease,” said George S. Vassiliou, FRCPath, MRCP, PhD, who is one of the joint leaders of the project and a consultant hematologist at Cambridge University Hospitals. “We hope to build on these findings to develop robust screening tests for identifying those at risk and drive research into how to prevent or stall progression towards AML. Our aspiration is that one day, AML prevention would provide a compelling alternative to treatment.”
Transfusion Medicine
Gastrointestinal flora: the culprit for severe lung damage after blood transfusion
Knowledge that the gastrointestinal flora affects both healthy physiological processes and various disease mechanisms has increased in recent years. A study conducted at Lund University is now published in one of the leading hematology journals, Blood Advances, and reveals a previously unknown link between the bacteria in the gut and acute lung injury after blood transfusions.
Researchers at Lund University in Sweden, in an international collaborative project, have now found a direct link between the gastrointestinal flora and lung disease in the setting of blood transfusions.
"We observed that the composition of the gastrointestinal flora drives the pathogenic immune response in the lungs during TRALI," says Rick Kapur, a post-doctoral researcher at Lund University, one of the participants behind the study.
The researchers compared two groups of mice where one group was kept in a strictly sterile environment, allowing the gastrointestinal flora to be minimally affected by external factors, whereas the other group was raised in a normal, less sterile environment.
"We saw that the mice kept in a more sterile environment were resistant to TRALI development while the less sterile-raised mice developed severe TRALI, says Professor John W. Semple, the lead investigator of the study at Lund University.
The composition of the gastrointestinal flora was demonstrated to be significantly different between the two groups of mice, as was determined by genetic sequencing of the stool in collaboration with the Centre for Translational Genomics (CTG) of Lund University. In addition, when the researchers wiped out the gastrointestinal flora with several different types of antibiotics, they saw that the mice that suffered from TRALI no longer developed the disease.
The researchers then transplanted stool from mice that developed TRALI into mice that were resistant to TRALI. After the stool transplantation, the resistant mice were also able to develop TRALI, which confirmed the link between the composition of the gastrointestinal flora and the onset of TRALI.
The researchers still need to clarify which specific gut bacteria are directly involved but the knowledge that intestinal bacteria may affect the lungs is a critical finding which may facilitate diagnostics and the development of potential new drugs. Additionally, the ability to be able to easily assess the risk for TRALI due to analysis of gastrointestinal flora is equally important, argue the researchers.
Microbiology
Imprint cytology: a useful screening test for diagnosis of Helicobacter pylori in resource poor settings
Helicobacter pylori diagnosis is a challenging task despite the availability of several diagnostic methods. In Sri Lanka, histological investigations are a main approach for H. pylori diagnosis. A drawback of this approach is the long turnaround time incurred due to the laborious preparations involved in specimen processing. Therefore a rapid low cost and simple method to diagnose H. pylori infection will enable initiation of treatment immediately.
Objective
The study aimed to compare the usefulness of two staining methods for imprint cytology for diagnosis of Helicobacter pylori infection. Gastric biopsy specimens (from dyspeptic patients attending routine upper gastrointestinal endoscopy) were placed on glass slides to obtain imprints. The imprints were stained with Toluidine blue and Giemsa stains separately and observed under ×400 magnification using a light microscope. Imprinted biopsies were sectioned and stained with H & E stain and Giemsa stain for histological analysis. Diagnosis of H. pylori infection in both imprint and histological sections were confirmed by a consultant pathologist. The sensitivity, specificity, positive predictive value and negative predictive value of each stain were calculated and benchmarked against histological diagnosis.
Results
Of the 55 dyspeptic patients enrolled in the study, 5 were positive for H. pylori by Toluidine blue stain and 4 by Giemsa stain. The sensitivity of Toluidine blue stain (57.1%) was higher than Giemsa stain (42.9%) while the specificity of both stains was equal (97.9%). Giemsa stain gave a better discrimination for identification of H. pylori bacteria among the mucosal background. Imprint cytology is a rapid, simple and cost effective diagnosis method that can supplement histological diagnosis.
Anatomic Pathology
MUSE Microscopy Does Histology Without Formalin Fixation
Scientists at the University of California at Davis (UC Davis) have developed a microscope that uses ultraviolet light (UV) to illuminate tissue samples. The UV microscope removes the need for traditional histology processes involved with preparation of tissue to produce conventional slides and makes it possible for anatomic pathologists to evaluate tissues without formalin fixation, according to a UC Davis news release.
“Here, we introduce a simple, non-destructive slide-free technique that, within minutes, provides high-resolution diagnostic histological images resembling those obtained from conventional hematoxylin and eosin histology,” the researchers wrote in their paper, published in Nature Biomedical Engineering.
The UV microscope relies on technology that UC Davis researchers dubbed MUSE, which stands for Microscopy with Ultraviolet Surface Excitation. According to the researchers, MUSE produces high-resolution images of biopsies and other fresh tissue samples that are ready for a pathologist’s review within minutes.
“MUSE eliminates any need for conventional tissue processing with formalin fixation, paraffin embedding, or thin-sectioning. It doesn’t require lasers, confocal, multiphoton, or optical coherence tomography instrumentation. And the simple technology makes it well-suited for deployment wherever biopsies are obtained and evaluated,” stated Richard Levenson, MD, MUSE Microscopy CEO, Professor, and Vice Chair for Strategic Technologies in the Department of Pathology and Laboratory Medicine at UC Davis, in the news release.
Cytology
HPV Testing More Effective Than Pap Test at Detecting Cervical Intraepithelial Neoplasia
Although cervical cancer is one of the most preventable cancers in the United States through early detection and treatment of abnormal cervical cell growth prior to cancer development, about 12,000 women are diagnosed with cervical cancer in the United States each year. Two traditional screening tests—the Pap (cytology-based) and HPV tests—are used to detect cervical cell changes as well as HPV. Research has shown that about “99.7% of all cervical cancers are associated with a persistent cervical infection with an oncogenic HPV genotype preceding the invasive tumor.”
To this end, a team of investigators, led by Gina Suzanne Ogilvie, MD, DrPH, of the University of British Columbia Faculty of Medicine, in Vancouver, Canada, conducted a randomized clinical trial (HPV FOCAL) which included more than 19,000 women who were recruited between January 2008 and May 2012. Those women who fit the study criteria of being between the ages of 25 and 65 (mean age, 45 years), with no recent clinical history of CIN2+, or no history of invasive cervical cancer or hysterectomy, no recent PAP (within the past year) and who were not taking immunosuppressive therapy were included in the study. Participants were randomized into either an intervention group (n = 9552) which received HPV testing, or a control group (n = 9457) which received liquid-based cytology (LBC) testing. Those patients in the HPV group who had negative results after the first round of testing returned for follow-up after 48 months, while patients tested with LBC who had negative results returned at 24, then 48 months.
At the end of the 48-month checkup period, both groups received HPV and LBC co-testing.
The results of the study indicated that at 48 months, patients in the intervention group had significantly fewer incidence rates for CIN3+ (2.3/1000; 95% CI; 1.5-3.5) versus patients in the control group (5.5/1000; 95% CI; 4.2-7.2), with a risk ratio of 0.42 (95% CI; 0.25-0.69).
Patients in the intervention group reported similarly significant reduced rates of CIN2+ incidence (5.0/1000; 95% CI; 3.8-6.7) versus patients in the control group (10.6/1000; 95% CI; 8.7-12.9) at 48 months. The CIN2+ risk ratio was 0.47 (95% CI; 0.34-0.67).
According to the investigators, participants who were HPV-negative at baseline had a significantly lower cumulative CIN3+ incidence at 48 months than women who were cytology-negative, with a risk ratio of 0.25 (95% CI; 0.13-0.48).
Based on these results, the investigators concluded that primary HPV testing is able to detect cervical neoplasia earlier and more accurately than cytology.
Molecular Genetics
Researchers reveal why CRISPR gene editing sometimes fails to work
Researchers from the University of Illinois at Chicago are the first to describe why CRISPR gene editing sometimes fails to work, and how the process can be made to be much more efficient.
CRISPR is a gene-editing tool that allows scientists to cut out unwanted genes or genetic material from DNA, and sometimes add a desired sequence or genes. CRISPR uses an enzyme called Cas9 that acts like scissors to cut out unwanted DNA. Once cuts are made on either side of the DNA to be removed, the cell either initiates repair to glue the two ends of the DNA strand back together, or the cell dies.
In a study published in the journal Molecular Cell, the researchers showed that when gene editing using CRISPR fails, which occurs about 15 percent of the time, it is often due to persistent binding of the Cas9 protein to the DNA at the cut site, which blocks the DNA repair enzymes from accessing the cut.
Researchers from the University of Illinois at Chicago are the first to describe why CRISPR gene editing sometimes fails to work, and how the process can be made to be much more efficient.
"We found that at sites where Cas9 was a 'dud' it stayed bound to the DNA strand and prevented the cell from initiating the repair process," Merrill said. The stuck Cas9 is also unable to go on to make additional cuts in DNA, thus limiting the efficiency of CRISPR, he said.
Merrill, UIC graduate student Ryan Clarke, and their colleagues also found that Cas9 was likely to be ineffective at sites in the genome where RNA polymerases -; enzymes involved in gene activity -; were not active. Further investigation revealed that guiding Cas9 to anneal to just one of the strands making up the DNA double helix promoted interaction between Cas9 and the RNA polymerase, helping to transform a "dud" Cas9 into an efficient genome editor.
Specifically, they found that consistent strand selection for Cas9 during genome editing forced the RNA polymerases to collide with Cas9 in such a way that Cas9 was knocked off the DNA.
The study findings are also significant because, in the genome editing process, the interaction between Cas9 and the DNA strand is now known to be the "rate-limiting step," said Merrill. This means that it is the slowest part of the process; therefore, changes at this stage have the most potential to impact the overall duration of genome editing.
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