Researchers conducting a comprehensive proteomics analysis of human aqueous humour samples identified 763 proteins – including 386 proteins detected for the first time – in this clear fluid that helps maintain pressure in the eye and nourishes the cornea and the lens. These proteins could have a role in disease processes affecting the eye and serve as valuable biomarkers for the development of diagnostics and drug candidates to improve visual health.

A team of researchers from the United States and India, led by Akhilesh Pandey, MD, PhD, Johns Hopkins University School of Medicine (Baltimore, MD) and Krishna Murthy, DO, MRCOphth (Lon) Institute of Bioinformatics (Bangalore, India), used high-resolution mass spectrometry to analyse and identify the proteins isolated from aqueous humour samples collected from 250 individuals. More than a third of the proteins were located outside of cells, in the extracellular matrix, and are involved in cell communication and signal transduction. Others have roles in cell growth, differentiation, and proliferation.

Among the proteins unique to this study are growth factors, immunomodulators, and proteins that regulate blood vessel formation. Other enzymes have a role in metabolism and the energy needs of ocular components such as the lens and cornea. For example, sorbitol dehydrogenase, one of the 386 novel proteins identified in the aqueous humour, plays an important role in the metabolism of glucose in the lens. EurekAlert

Unreliable oestrogen measurements have had a negative impact on the treatment of and research into many hormone-related cancers and chronic conditions. To improve patient care, a panel of medical experts has called for accurate, standardized oestrogen testing methods in a statement published in the Endocrine Society’s Journal of Clinical Endocrinology & Metabolism (JCEM).
The panel’s recommendations are the first to address how improved testing methods can affect clinical care, and were developed based on discussions at an oestrogen measurement workshop hosted by the Endocrine Society, AACC and the Partnership for Accurate Testing of Hormones (PATH).

Oestrogen is primarily produced in the ovaries and is also produced in small amounts by the adrenal glands, which is why men as well as women have oestrogen in their bodies. It is critical for fertility in women, and also plays a role in many health conditions, from precocious puberty to cancers of the breast, ovary, prostate and liver. Accurate blood tests for oestrogen are necessary to diagnose patients with these conditions and ensure they receive appropriate, effective treatment. Many medical studies also rely on oestrogen tests, such as research assessing the connection between oestrogen levels and the risk of breast or prostate cancer.

“Accurate data on patients’ oestrogen levels are needed to ensure appropriate and effective patient care, reduce the need for retesting, and enable clinicians to implement the latest research in patient care,” said one of the authors and co-chair of the PATH Steering Committee, Hubert Vesper, PhD. “Research studies, however, found high inaccuracies among different oestrogen tests, especially when the test is measuring low oestrogen levels in postmenopausal women, men and children.”

The expert panel called for improving the accuracy of measurements through standardization, and recommended clinicians, researchers and public health officials support standardization programs like CDC’s and other efforts to ensure oestrogen measurement is accurate and consistent.

The panel also advised clinicians and researchers to consider the purpose of the test when selecting an oestrogen measurement method. Clinicians and researchers currently use several methods to measure oestrogen, including mass spectrometry and immunoassays. The experts agreed both methods are valid, but that one may be more effective than the other depending on the situation. For instance, mass spectrometry—the more expensive, but also more sensitive testing method—may be appropriate in people who tend to have low oestrogen levels, including postmenopausal women and children beginning puberty.

Additionally, the experts recommended that medical journals require authors to fully explain the oestrogen measurement testing methods used in studies. Ensuring researchers explain the processes they used will help the field move toward standardized methods. The Endocrine Society

Thoracic aortic aneurysm and dissection (TAAD), an enlargement or tearing of the walls of the aorta in the chest, is, together with abdominal aortic aneurysms, responsible for about 2% of all deaths in Western countries. The aorta is the largest artery in the body, and carries blood from the heart. About one out of every five patients with TAAD has a family member with the same disorder, therefore indicating a genetic cause. However, the relevant genetic mutations discovered so far only explain about 30% of all cases. Through the study of a large family with TAAD features, an international team of genetic researchers have now discovered that a mutation in the TGFB3 gene is also responsible for the condition.

Elisabeth Gillis, MSc, a PhD student in the Centre for Medical Genetics at Antwerp University Hospital, Antwerp, Belgium, explains that she and colleagues from seven other countries are the first to link this particular genetic mutation to serious aortic disorders. This is important, she says, because it means that the TGFB3 gene can be included in diagnostic screening. ‘Armed with this knowledge, we can screen patients with symptoms of TAAD, and also family members without symptoms. Early identification of a risk of aortic aneurysm formation will allow us to implement preventive treatment with medication aimed at slowing down the process of aneurysm and, ultimately, replacement of the aorta before a significant risk of dissection arises’, she will say.

An aortic aneurysm occurs where there is a weakness in the walls of the aorta, creating an outward bulge. Weakness in the aorta is dangerous, because it can lead to rupture (dissection) which is life-threatening.

The researchers studied 9 patients from a large Flemish-Dutch family with the cardiovascular, skeletal and facial features typical of a form of TAAD, called Loeys-Dietz syndrome. They screened DNA from each family member without finding any genetic mutations known at that stage to be connected with TAAD. However, further investigation revealed two candidate genomic regions that appeared to be involved, one of which contained the TGBF3 gene. ‘This gene was an obvious candidate because it has previously been shown that the TGFbeta-signalling pathway has a key role in the formation of aortic aneurysm,’ says Ms Gillis.

After sequencing the gene, the researchers identified a mutation that was present in all affected family members. Finally, 470 TAAD patients were screened for TGFB3 mutations, and causal mutations were found in ten other families.

‘This is an important finding because incidence of TAADs may be much higher than currently reported,’ says Ms Gillis. ‘Acute aortic dissections may be disguised as heart attacks, and we know that the genetic component of TAAD is strong – in about 20% of patients, it is also found in family members. Therefore anything we can do to enable early identification of people at risk will help. However, aortic aneurysm formation is not yet fully understood, so reversing the risk of dissections remains a challenge, even though effective treatments are available.’ EurekAlert

A team of scientists, part of the international effort to curb further spread of the Ebola virus in Sierra Leone, has released its first dataset of the virus’ genetic structure online. The dataset will allow the global scientific community to monitor the pathogen’s evolution in real-time and conduct research that can lead to more effective strategies against further outbreaks.

The team of British scientists, funded by the Wellcome Trust, is using semi-conductor next-generation sequencing technology developed by Thermo Fisher Scientific to generate data in a lab facilitated by Public Health England and International Medical Corps. The genetic analysis is being made freely available to the scientific community.

Since the first reported case in March 2014, the Ebola outbreak has claimed nearly 11,000 lives in West African countries. Professor Ian Goodfellow, Head of Virology at the University of Cambridge, travelled to Sierra Leone in December last year and then again in March this year to help set up a new diagnostics centre attached to an Ebola Treatment Centre in one of the country’s worst affected parts. He returned a third time, together with his postdoc Dr Armando Arias, to study the virus at a molecular level using the sequencing technology.

“Sequencing the genome of a virus can tell us a lot about how it spreads and changes as it passes from person to person. While this information is invaluable to researchers, the rapid sharing of data does not always occur,” said Professor Paul Kellam at the Wellcome Trust Sanger Institute, who is leading the team to map the genomic data captured by Professof Goodfellow and colleagues. “It used to take months to process samples that had to be brought back to labs in the UK for analysis. Having sequencing capabilities on the ground helps generate data in a matter of days or at the longest weeks, which should have a profound impact on how the Ebola virus is researched and inevitably addressed on a global scale.”

Rapid sequencing enables epidemiologists to decipher the source of individual strains, and helps eliminate the need to rely upon Ebola patients to tell them how and where they contracted the virus, as different strains can be tracked as they are transmitted from person to person.

“Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks,” said Goodfellow. “My hope is that this technology will be used by the next generation of Sierra Leonean scientists and researchers to help provide a sustainable research and surveillance system in the future.” University of Cambridge

Scientists from the Icahn School of Medicine at Mount Sinai have developed a new technique to more precisely analyse bacterial populations, to reveal epigenetic mechanisms that can drive virulence.  The new methods hold the promise of a potent new tool to offset the growing challenge of antibiotic resistance by bacterial pathogens.

The information content of the genetic code in DNA is not limited to the primary nucleotide sequence of A’s, G’s, C’s and T’s. Individual DNA bases can be chemically modified, with significant functional consequences.  In the bacterial kingdom, the most prevalent base modifications are in the form of DNA methylations, specifically to adenine and cytosine residuals.  Beyond their participation in host defence, increasing evidence suggests that these modifications also play important roles in the regulation of gene expression, virulence and antibiotic resistance.

The research team employed the PacBio RS II system which can collect data on base modifications simultaneously as it collects DNA sequence data. PacBio’s single molecule, real-time sequencing enables the detection of N6-methyladenine and 4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing methods for studying bacterial methylomes rely on a population-level consensus that lack the single-cell resolution required to observe epigenetic heterogeneity.

“We created a technique for the detection and phasing of DNA methylation at the single molecule level.  We found that a typical clonal bacterial population that would otherwise be considered homogeneous using conventional techniques has epigenetically distinct subpopulations with different gene expression patterns’ said Gang Fang, PhD, Assistant Professor of Genetics and Genomics at the Icahn School of Medicine at Mount Sinai and senior author of the study.  “Given that phenotypic heterogeneity within a bacterial population can increase its advantage of survival under stress conditions such as antibiotic treatment, this new technique is quite promising for future treatment of bacterial pathogens, as it enables de novo detection and characterization of epigenetic heterogeneity in a bacterial population.”

The researchers studied seven bacterial strains, demonstrating the new technique reveals distinct types of epigenetic heterogeneity. For Helicobacter pylori, a pathogenic bacterium that colonizes over 40% of the world population and is associated with gastric cancer, the team discovered that epigenetic heterogeneity can quickly emerge as a single cell divides, and different subpopulations with distinct methylation patterns have distinct gene expressions patterns. This may have contributed to the increasing rate of antibiotic resistance of Helicobacter pylori.

“The application of this new technique will enable a more comprehensive characterization of the functions of DNA methylation and their impact on bacterial physiology.  Resolving nucleotide modifications at the single molecule, single nucleotide level, especially when integrated with other single molecule- or single cell-level data, such as RNA and protein expression, will help resolve regulatory relationships that govern higher order phenotypes such as drug resistance” said Eric Schadt, PhD, Founding Director of the Icahn Institute and Professor of Genomics at the Icahn School of Medicine at Mount Sinai.  “The approach we developed can also be used to analyze DNA viruses and human mitochondrial DNA, both of which present significant epigenetic heterogeneity.” Mount Sinai Health System