The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies

Maternal plasma contains circulating cell-free DNA fragments originating from both the mother and the placenta. The proportion derived from the placenta is known as the fetal fraction. When measured between 10 and 20 gestational weeks, the average fetal fraction in the maternal plasma is 10% to 15% but can range from under 3% to over 30%. Screening performance using next-generation sequencing of circulating cell-free DNA is better with increasing fetal fraction and, generally, samples whose values are less than 3% or 4% are unsuitable. Three examples of the clinical impact of fetal fraction are discussed. First, the distribution of test results for Down syndrome pregnancies improves as fetal fraction increases, and this can be exploited in reporting patient results. Second, the strongest factor associated with fetal fraction is maternal weight; the false negative rate and rate of low fetal fractions are highest for women with high maternal weights. Third, in a mosaic, the degree of mosaicism will impact the performance of the test because it will reduce the effective fetal fraction. By understanding these aspects of the role of fetal fraction in maternal plasma DNA testing for aneuploidy, we can better appreciate the power and the limitations of this impressive new methodology. © 2013 John Wiley & Sons, Ltd.     

Diurnal variations in bacterial and viral production in Cochin estuary, India

Microbes play a central role in the decomposition and remineralization of organic matter and recycling of nutrients in aquatic environments. In this study, we examined the influence of physical, chemical, and biological parameters on the rate of bacterial production (BP) and viral production (VP) with respect to primary production over a diurnal period in Cochin estuary. Time series measurements were made every 2 h for 12 h (6 a.m.–6 p.m.) during periods of low and high salinities. The light intensity as photosynthetically active radiation, temperature, salinity, nutrients like NO₃–N, SiO₄–Si, and PO₄–P, and chlorophyll a (Chl a) were measured along with BP, VP, and net primary production (NPP). NPP showed a strong positive correlation with light and Chl a (r ²?=?0.56 and 0.47, respectively), while VP showed a strong positive correlation with light, salinity, and Chl a (r ²?=?0.37, 0.58, and 0.37, respectively) and a negative correlation with BP (r ²?=??0.39) at P?≤?0.05. We observed a diurnal pattern in BP but did not have any significant correlation with light. Similar diurnal pattern was seen in VP, the peak of which was in succession with BP, suggesting that virus-mediated lysis plays an important role in loss processes of bacteria in Cochin estuary. The results of our study highlight the light-dependent and physicochemical-dependent diurnal variation in virioplankton production in a tropical estuarine ecosystem.     

SITING OF A WATER POLLUTION CONTROL FACILITY AT JAMESTOWN,RHODE ISLAND1

ABSTRACT: The town of Jamestown, Rhode Island, located on Conanicut Island in Narragansett Bay, is constructing a secondary treatment plant in order to comply with NPDES regulations. Twelve candidate sites for the plant and marine outfall were initially proposed, and ability to meet State water quality standards at these sites was evaluated using an EPA buoyant plume model. A final outfall site, Taylor Point, was selected by the Town from among the sites considered acceptable. Taylor Point was then subjected to field hydrographic studies including drogue tracking, current recordings, and tracer dye surveys. Results of the measurement program served as input to a two-dimensional effluent dispersion model which predicted excess BOD, coliform, and suspended solids resulting from effluent discharge off Taylor Point. The model predictions demonstrated that State water quality standards can be maintained outside the initial discharge plume.     

Symbiotic bacteria in hornet pupal silk

The silk weave spun by hornet larvae before undergoing pupal metamorphosis is composed of fibers and sheets, both containing symbiotic bacteria. The bacteria are secreted from the silk gland and are glued to the secreted silk, which is made up of amino-acid polymers. In the dark, it possesses at first an electric current amounting to several hundred nanoamperes (nA) (i.e., a thermoelectric property), and a high electric capacitance of up to several milliFarads (mF). This electrical charge is used gradually by the developing pupa. The symbiotic bacteria penetrate through slits in the coat of the silk fibers to the core or into pockets in the sheets, where they gradually digest parts of the silk weave, thereby nullifying its mechanical properties and facilitating in due time the egress of the imago from the puparium.     

Noninvasive fetal genome sequencing: a primer

We recently demonstrated whole genome sequencing of a human fetus using only parental DNA samples and plasma from the pregnant mother. This proof-of-concept study demonstrated how samples obtained noninvasively in the first or second trimester can be analyzed to yield a highly accurate and substantially complete genetic profile of the fetus, including both inherited and de novo variation. Here, we revisit our original study from a clinical standpoint, provide an overview of the scientific approach, and describe opportunities and challenges along the path toward clinical adoption of noninvasive fetal whole genome sequencing. © 2013 John Wiley & Sons, Ltd.