Progressive Domain Segregation in Early Embryonic Development and Underlying Correlation to Genetic and Epigenetic Changes

Chromatin undergoes drastic structural organization and epigenetic reprogramming during embryonic development. We present here a consistent view of the chromatin structural change, epigenetic reprogramming, and the corresponding sequence-dependence in both mouse and human embryo development. The two types of domains, identified earlier as forests (CGI-rich domains) and prairies (CGI-poor domains) based on the uneven distribution of CGI in the genome, become spatially segregated during embryonic development, with the exception of zygotic genome activation (ZGA) and implantation, at which point significant domain mixing occurs. Structural segregation largely coincides with DNA methylation and gene expression changes. Genes located in mixed prairie domains show proliferation and ectoderm differentiation-related function in ZGA and implantation, respectively. The chromatin of the ectoderm shows the weakest and the endoderm the strongest domain segregation in germ layers. This chromatin structure difference between different germ layers generally enlarges upon further differentiation. The systematic chromatin structure establishment and its sequence-based segregation strongly suggest the DNA sequence as a possible driving force for the establishment of chromatin 3D structures that profoundly affect the expression profile. Other possible factors correlated with or influencing chromatin structures, including transcription, the germ layers, and the cell cycle, are discussed for an understanding of concerted chromatin structure and epigenetic changes in development.

Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes

Chromatin undergoes drastic structural organization and epigenetic reprogramming during embryonic development. We present here a consistent view of the chromatin structural change, epigenetic reprogramming and the corresponding sequence dependence in both mouse and human embryo development. The two types of domains, identified earlier as forests and prairies, become spatially segregated during embryonic development, with the exception of zygotic genome activation (ZGA) and implantation, at which notable domain mixing occurs. Structural segregation largely coincides with DNA methylation and gene expression changes. Genes located in mixed prairie domains show proliferation and ectoderm differentiation-related function in ZGA and implantation, respectively. Chromatin of ectoderm shows the weakest and endoderm the strongest domain segregation in germ layers. This chromatin structure difference between different germ layers generally enlarges in further differentiation. The systematic chromatin structure establishment and its sequence-based segregation strongly suggest DNA sequence as a possible driving force for the establishment of chromatin 3D structures which affect profoundly the expression profile. Other possible factors correlated with/influencing chromatin structures, including temperature, germ layers, and cell cycle, are discussed for an understanding of concerted chromatin structure and epigenetic changes in development.

Birds suppress pests in corn but release them in soybean crops within a mixed prairie/agriculture system

Birds provide ecosystem services (pest control) in many agroecosystems and have neutral or negative ecological effects (disservices) in others. Large-scale, conventional row crop agriculture is extremely widespread globally, yet few studies of bird effects take place in these agroecosystems. We studied indirect effects of insectivorous birds on corn and soybean crops in fields adjacent to a prairie in Illinois (USA). We hypothesized that prairie birds would forage for arthropods in adjacent crop fields and that the magnitude of services or disservices would decrease with distance from the prairie. We used bird-excluding cages over crops to examine the net effect of birds on corn and soybean grain yield. We also conducted DNA metabarcoding to identify arthropod prey in fecal samples from captured birds. Our exclosure experiments revealed that birds provided net services in corn and net disservices in soybeans. Distance from prairie was not a significant predictor of exclosure treatment effect in either crop. Many bird fecal samples contained DNA from both beneficial arthropods and known economically significant pests of corn, but few economically significant pests of soybeans. Song Sparrows (Melospiza melodia), one of our most captured species, most commonly consumed corn rootworms, an economically significant pest of corn crops. We estimated that birds in this system provided a service worth approximately US $275 ha−1 in corn yield gain, and a disservice valued at approximately $348 ha−1 in soybean yield loss. Our study is the first to demonstrate that birds can provide substantial and economically valuable services in field corn, and disservices in soybean crops. The contrasting findings in the 2 crop systems suggest a range of bird impacts within widespread agroecosystems and demonstrate the importance of quantifying net trophic effects.

Influence of streambank fencing on vegetation and soil of the Mixed prairie component in a complex corridor pasture

A 5 yr (2011–2015) field study was conducted to test the hypothesis that streambank fencing had a significant effect on selected vegetation and soil properties of the Mixed prairie component of a complex corridor pasture. The grazing treatments [ungrazed (UG) – periodic grazing (PG)] inside the corridor pasture were 11 yr (2001–2012) of cattle exclusion (UG), followed by 3 yr (2013–2015) of periodic grazing (PG) when the riparian soil was dry. A control treatment outside the fencing was continuous grazing (CG). Selected vegetation and soil properties were measured over the growing season at 10 paired locations in each treatment (nonreplicated) pasture over 5 yr (2011–2015), and rangeland health was measured in 2011. The UG–PG treatment significantly (P ≤ 0.10) increased the total biomass by 2- to 5-fold in all 5 yr compared with CG treatment and improved the rangeland health score of the UG phase of the UG–PG (63%) treatment compared with the CG treatment (50%) in 2011. It also significantly reduced surface soil temperature by 2.2–5.2 °C, significantly increased volumetric water content of the surface soil by 7%–10% in 3 of 5 yr, and significantly increased surface soil CO2 efflux (instantaneous) by 17%–60% in all 5 yr. Overall, the UG–PG treatment improved rangeland health, increased total biomass, soil water, and soil CO2 efflux of the Mixed prairie, but decreased soil temperature compared with the CG treatment. Excessive dead biomass, greater fire risk, and an increase in noxious weeds caused by cattle exclusion suggested that periodic grazing may be the preferred option.