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.     

Low back pain among residential carpenters: ergonomic evaluation using OWAS and 2D compression estimation.

Occupational low back pain (LBP) remains a leading safety and health challenge. This cross-sectional investigation measured the prevalence of LBP in residential carpenters and investigated ergonomic risk factors. Ninety-four carpenters were investigated for LBP presence and associated risk factors. Ten representative job-tasks were evaluated using the Ovako Working Posture Analysis System (OWAS) and ErgoMaster 2D software to measure elements of posture, stress, and risk. Job-tasks were found to differ significantly for total lumbar compression and shear at peak loading (p < .001), ranging from 2 956 to 8 606 N and 802 to 1 974 N respectively. OWAS indicated that slight risk for injury was found in 10 job-tasks while distinct risk was found in 7 of the 10 job-tasks. Seven of the 10 job-tasks exceeded the National Institute for Occupational Safety and Health (NIOSH) action limit of 3 400 N for low back loading. The point prevalence for LBP was 14% while the annual prevalence was 38%.     

Livestock excreta management through vermicomposting using an epigeic earthworm Eisenia foetida

In India, millions of tones of livestock excreta are produced. Our study explores the potential of an epigeic earthworm Eisenia foetida to compost different livestock excreta (cow, buffalo, horse, donkey, sheep, goat and camel) into value added product (vermicompost) at the laboratory scale. Vermicomposting resulted in lowering of pH, electrical conductivity, potassium and C:N ratio and increase in nitrogen and phosphorus contents. Total K was lower in the final cast than in the initial feed. C:N ratios of the vermicomposts ranged from 16.2 ± 2.17 to 75.4 ± 6.84. Microbial activity measured as dehydrogenase activity in buffalo, donkey and camel wastes increased with time up to day 90. But in sheep and goat wastes, maximum dehydrogenase activity was recorded on day 60 and decreased thereafter. The cocoons and hatchlings production by Eisenia foetida in different excreta were also investigated. The greatest number and biomass of hatchlings was recorded in horse excreta followed by cow, goat and sheep excreta. Thus, cow, horse, sheep and goat excreta show potential as good substrates in vermicomposting using Eisenia foetida, although further research is required to explore the feasibility of use of buffalo, donkey and camel excreta in combination with cow/sheep/goat excreta.     

Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia

Several genotypic methods have been developed for determining the host origin of fecal bacteria in contaminated waters. Some of these methods rely on a host origin database to identify environmental isolates. It is not well understood to what degree these host origin isolates are geographically variable (i.e., cosmopolitan or endemic). This is important because a geographically limited host origin database may or may not be universally applicable. The objective of our study was to use one genotypic method, ribotyping, to determine the geographic variability of the fecal bacterium, Escherichia coli, from one location in Idaho and three locations in Georgia for cattle (Bos taurus), horse (Equus caballus), swine (Sus scrofa), and chicken (Gallus gallus domesticus). A total of 568 fecal E. coli isolates from Kimberly, ID (125 isolates), Athens, GA (210 isolates), Brunswick, GA (102 isolates), and Tifton, GA (131 isolates), yielded 213 ribotypes. The percentage of ribotype sharing within an animal species increased with decreased distance between geographic locations for cattle and horses, but not for swine and chicken. When the E. coli ribotypes among the four host species were compared at one location, the percent of unshared ribotypes was 86, 89, 81, and 79% for Kimberly, Athens, Brunswick, and Tifton, respectively. These data suggest that there is good ribotype separation among host animal species at each location. The ability to match environmental isolates to a host origin database may depend on a large number of environmental and host origin isolates that ideally are not geographically separated.     

Understanding and predicting ecological dynamics: are major surprises inevitable?

Ecological surprises, substantial and unanticipated changes in the abundance of one or more species that result from previously unsuspected processes, are a common outcome of both experiments and observations in community and population ecology. Here, we give examples of such surprises along with the results of a survey of well-established field ecologists, most of whom have encountered one or more surprises over the course of their careers. Truly surprising results are common enough to require their consideration in any reasonable effort to characterize nature and manage natural resources. We classify surprises as dynamic-, pattern-, or intervention-based, and we speculate on the common processes that cause ecological systems to so often surprise us. A long-standing and still growing concern in the ecological literature is how best to make predictions of future population and community dynamics. Although most work on this subject involves statistical aspects of data analysis and modeling, the frequency and nature of ecological surprises imply that uncertainty cannot be easily tamed through improved analytical procedures, and that prudent management of both exploited and conserved communities will require precautionary and adaptive management approaches.     

Mitigation of methane emission from an old unlined landfill in Klintholm,Denmark using a passive biocover system

Methane generated at landfills contributes to global warming and can be mitigated by biocover systems relying on microbial methane oxidation. As part of a closure plan for an old unlined landfill without any gas management measures, an innovative biocover system was established. The system was designed based on a conceptual model of the gas emission patterns established through an initial baseline study. The study included construction of gas collection trenches along the slopes of the landfill where the majority of the methane emissions occurred. Local compost materials were tested as to their usefulness as bioactive methane oxidizing material and a suitable compost mixture was selected. Whole site methane emission quantifications based on combined tracer release and downwind measurements in combination with several local experimental activities (gas composition within biocover layers, flux chamber based emission measurements and logging of compost temperatures) proved that the biocover system had an average mitigation efficiency of approximately 80%. The study showed that the system also had a high efficiency during winter periods with temperatures below freezing. An economic analysis indicated that the mitigation costs of the biocover system were competitive to other existing greenhouse gas mitigation options.