Fetal fraction and noninvasive prenatal testing: What clinicians need to know

The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a “plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.     

CHANGING NEAR‐STREAM LAND USE AND RWER CHANNEL MORPHOLOGY IN THE VENEZUELAN ANDES1

ABSTRACT: The shape of a river channel is linked to surrounding land use through interacting hydrologic and geologic processes. This study analyzes the relationship between the change in near‐stream land use and the shape of the adjacent river channel over time. Three watersheds in the foothills of the Venezuelan Andes that have experienced differing degrees of development were studied to determine river channel width, sinuosity, and position relative to surrounding land use. Change in land use over time was obtained from multiple‐date aerial photographs (1946 and 1980) referenced to 1996 Landsat Thematic Mapper (TM) satellite imagery, and verified by field inspection. Measurements of land‐use type and amount and river channel morphology from the two dates were made using geographic information system (GIS) methods. The three watersheds differed in the extent of deforestation, the location of remaining forested land, and how much land‐use change had already occurred by 1946. Change in river channel morphology was greatest at the most deforested sites. Valley shape and channel constraint also had a discernible effect on change in channel morphology. This study introduces a method for analyzing change in coupled terrestrial‐aquatic systems based on multiple‐date, remotely sensed data and GIS analysis of spatial properties. The results document human impacts on river channels through a comparison of multiple watersheds over a 35‐year time interval.     

Long-term effects of amendment with liquid swine manure on proton binding behavior of soil humic substances

The acid-base properties of humic acids (HAs) and fulvic acids (FAs) isolated from liquid swine manure (LSM), soils amended with either 90 or 150 m(3)ha(-1)year(-1) of LSM for 7 years, and the corresponding unamended control soil were investigated by a current potentiometric titration method. The non-ideal competitive adsorption (NICA)-Donnan model for proton binding by two classes of binding sites (i.e., carboxylic- and phenolic-type groups) was fit to titration data, and a set of fitting parameters was obtained for each HA and FA sample. The NICA-Donnan model was shown to describe with a great degree of accuracy the behavior of experimental titration datasets, and highlighted important differences in the acid-base properties of the HAs and FAs examined. When compared to the unamended soil HA and FA, LSM-HA and LSM-FA, had smaller acidic functional group contents, larger proton binding affinities of both carboxylic- and phenolic-type groups, smaller heterogeneity of carboxylic-type groups, and smaller, in the case of HA, or similar, in the case of FA, heterogeneity of phenolic-type groups. Amendment with LSM caused a decrease of acidic functional group contents and a slight increase of proton binding affinities of carboxylic- and phenolic-type groups of soil HAs and FAs. Further, LSM application induced a decrease of the heterogeneity of carboxylic-type groups, whereas appeared not to affect substantially the heterogeneity of phenolic-type groups of LSM-amended soil HAs and FAs. These effects were more evident for HAs than for FAs and tended to slightly increase with increasing LSM amendment rate.     

Assessment of the environmental contamination with long-lived radionuclides around an operating RBMK reactor station

The presence of man-made gamma emitting radionuclides in the region within 32km radius of the Ignalina NPP/Lithuania has been investigated during the period 2001-2004, prior to the closure of the first of the two operating RBMK 1500-type reactors. Gamma spectrometric measurements of various terrestrial and aquatic plants as well as of soil samples showed moderate environmental contamination with the fission product (137)Cs and with the neutron activation products (60)Co and (54)Mn. Traces of the activation products (65)Zn and (110m)Ag were found in the nearest vicinity of the NPP. Activity concentrations were inhomogeneously distributed in the area of interest. Moss and algae samples showed the highest uptake of radionuclides. In addition to the gamma spectrometric measurements, the levels of (14)C were determined in the same bio-indicator samples using accelerator mass spectrometry.     

Polychlorinated biphenyl (PCB) residues in European roe deer (Capreolus capreolus) and red deer (Cervus elaphus) from north-western Poland

The purpose of this study was to evaluate polychlorinated biphenyls (PCBs) contamination levels in roe and red deer from north-western Poland and to assess environmental pollution in this area. A quantitative analysis was conducted using a capillary gas chromatography/mass spectrometry method. The mean concentrations of ΣPCBs (sum of PCBs: 28, 52, 101, 138, 153, 180) in liver samples were 30.24±12.35 ng·g^?1 of lipid weight (l.w.) in roe deer and 60.13±14.23 ng·g^?1 l.w. in red deer, compared with 24.21±10.02 and 45.22±9.77 ng·g^?1 in the lungs of roe and red deer, respectively. PCBs 138, 153 and 180 were the dominant congeners in the liver samples of the analysed animals, whereas PCB 138 and 153 in the lungs. TEQs levels calculated for only dioxin-like PCBs were low: 0.32 and 0.29 pg WHO-PCB-TEQ·g^?1 fat in liver of red deer and roe deer, respectively. The mean PCB concentrations obtained in our study for organs of roe deer and red deer were several times lower than those reported elsewhere. These findings show that the investigated roe and red deer originated from an area with low levels of PCB contamination.     

The Effects of Blister Rust on Post-Fire Regeneration of Whitebark Pine: The Sundance Burn of Northern Idaho (U.S.A.)

In the northern Rocky Mountains, whitebark pine ( Pinus albicaulis ) is rapidly declining as a result of previous fire exclusion policies, mountain pine beetle ( Dendroctonus ponderosae ) outbreaks, and white pine blister rust ( Cronartium ribicola ). Blister rust is potentially the most destructive agent, killing seedlings, cone-bearing branches, and, eventually, mature trees. We examined densities of whitebark pine regeneration and the incidence and severity of blister-rust infection of seedlings and saplings in the 25-year-old Sundance Burn in the Selkirk Range of northern Idaho, an area heavily infected by blister rust. We found that the mean regeneration density of whitebark pine was significantly lower than that of two other comparably aged burns in western Montana. The low density was attributed to the severe damage to the seed source on the burn perimeter, resulting from previous infestation of mountain pine beetle and blister rust. Overall, 29% of the whitebark pine regeneration in the Sundance Burn was infected by blister rust. Age and height of seedlings were important predictors of incidence of infection, and height was the most important predictor of severity of infection. Thus, as seedlings grow larger, they present a bigger target to airborne blister-rust spores. Because of the lack of seed production in the adjacent forest and expected mortality, regeneration of whitebark pine in the Sundance Burn will be slow. In areas of northern Idaho and northwestern Montana affected by blister rust and pine beetle, prescribed fires for managing whitebark pine ecosystems should be restricted to small areas or should require plantings of rust-resistant seedlings.     

USE OF SYNOGRAPHIC TECHNIQUES IN RESEARCH AND DISSEMINATION OF HYDROLOGICAL INFORMATION1

ABSTRACT: Application of synographic techniques to four separate nonrelated research tasks demonstrated the usefulness of such an approach in interpreting and communicating hydrologic survey data especially when large geographic areas are involved. Nutrient exchange and biotic indicators in coastal estuaries were analyzed to determine residence times in different seasons of the year. Man induced changes in urban runoff patterns were shown to increase the probability of flooding with different recurrences of storm events. Nitrate and indicator bacteria in private wells were analyzed on a county-wide basis to determine the sources and extent of natural occurrence versus contamination origins. Water wells and the surface supply of metropolitan Houston were analyzed for sodium content to assist citizens and physicians with data which are needed for derivation of sodium restricted therapeutic diets.