MODIS-Based Fractional Crop Mapping in the U.S. Midwest with Spatially Constrained Phenological Mixture Analysis

Since the 2000s, bioenergy land use has been rapidly expanded in U.S. agricultural lands. Monitoring this change with limited acquisition of remote sensing imagery is difficult because of the similar spectral properties of crops. While phenology-assisted crop mapping is promising, relying on frequently observed images, the accuracies are often low, with mixed pixels in coarse-resolution imagery. In this paper, we used the eight-day, 500 m MODIS products (MOD09A1) to test the feasibility of crop unmixing in the U.S. Midwest, an important bioenergy land use region. With all MODIS images acquired in 2007, the 46-point Normalized Difference Vegetation Index (NDVI) time series was extracted in the study region. Assuming the phenological pattern at a pixel is a linear mixture of all crops in this pixel, a spatially constrained phenological mixture analysis (SPMA) was performed to extract crop percent covers with endmembers selected in a dynamic local neighborhood. The SPMA results matched well with the USDA crop data layers (CDL) at pixel level and the Crop Census records at county level. This study revealed more spatial details of energy crops that could better assist bioenergy decision-making in the Midwest

Ex Vivo Expansion of Human Hematopoietic Stem Cells by Garcinol, a Potent Inhibitor of Histone Acetyltransferase

BACKGROUND: Human cord blood (hCB) is the main source of hematopoietic stem and progenitor cells (HSCs/PCs) for transplantation. Efforts to overcome relative shortages of HSCs/PCs have led to technologies to expand HSCs/PCs ex vivo. However, methods suitable for clinical practice have yet to be fully established. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we screened biologically active natural products for activity to promote expansion of hCB HSCs/PCs ex vivo, and identified Garcinol, a plant-derived histone acetyltransferase (HAT) inhibitor, as a novel stimulator of hCB HSC/PC expansion. During a 7-day culture of CD34(+)CD38(-) HSCs supplemented with stem cell factor and thrombopoietin, Garcinol increased numbers of CD34(+)CD38(-) HSCs/PCs more than 4.5-fold and Isogarcinol, a derivative of Garcinol, 7.4-fold. Furthermore, during a 7-day culture of CD34(+) HSCs/PCs, Garcinol expanded the number of SCID-repopulating cells (SRCs) 2.5-fold. We also demonstrated that the capacity of Garcinol and its derivatives to expand HSCs/PCs was closely correlated with their inhibitory effect on HAT. The Garcinol derivatives which expanded HSCs/PCs inhibited the HAT activity and acetylation of histones, while inactive derivatives did not. CONCLUSIONS/SIGNIFICANCE: Our findings identify Garcinol as the first natural product acting on HSCs/PCs and suggest the inhibition of HAT to be an alternative approach for manipulating HSCs/PCs

Mapping Soil Alkalinity and Salinity in Northern Songnen Plain, China with the HJ-1 Hyperspectral Imager Data and Partial Least Squares Regression

In arid and semi-arid regions, identifying and monitoring of soil alkalinity and salinity are in urgently need for preventing land degradation and maintaining ecological balances. In this study, physicochemical, statistical, and spectral analysis revealed that potential of hydrogen (pH) and electrical conductivity (EC) characterized the saline-alkali soils and were sensitive to the visible and near infrared (VIS-NIR) wavelengths. On the basis of soil pH, EC, and spectral data, the partial least squares regression (PLSR) models for estimating soil alkalinity and salinity were constructed. The R2 values for soil pH and EC models were 0.77 and 0.48, and the root mean square errors (RMSEs) were 0.95 and 17.92 dS/m, respectively. The ratios of performance to inter-quartile distance (RPIQ) for the soil pH and EC models were 3.84 and 0.14, respectively, indicating that the soil pH model performed well but the soil EC model was not considerably reliable. With the validation dataset, the RMSEs of the two models were 1.06 and 18.92 dS/m. With the PLSR models applied to hyperspectral data acquired from the hyperspectral imager (HSI) onboard the HJ-1A satellite (launched in 2008 by China), the soil alkalinity and salinity distributions were mapped in the study area, and were validated with RMSEs of 1.09 and 17.30 dS/m, respectively. These findings revealed that the hyperspectral images in the VIS-NIR wavelengths had the potential to map soil alkalinity and salinity in the Songnen Plain, China

Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting

Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10) is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii), but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus), suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR) associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5′ region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation

A Multiphase Strategy for Realizing Green Cathodoluminescence in 12CaO·7Al2O3–CaCeAl3O7:Ce3+,Tb3+ Conductive Phosphor

A multiphase strategy is proposed and successfully applied to make the insulating green phosphor CaCeAl3O7:Tb3+ conductive in the form of 12CaO·7Al2O3–CaCeAl3O7:Ce3+,Tb3+. The phosphor shows bright green-light emission with a short lifetime (2.51 ms) under low-voltage electron beam excitation (3 kV). The green photo- and cathodoluminescence from 5D4–7FJ (J = 6, 5, 4, 3) transitions of Tb3+ are significantly enhanced in comparison with pure C12A7:Tb3+. It was confirmed that this enhancement is the consequence of the joint effects of energy transfer from Ce3+ to Tb3+ and broadening of the absorption spectrum of Ce3+ due to the existence of multiple phases. In particular, under 800 V electron beam excitation, cathodoluminescence is improved by the modified electrical conductivity of the phosphor. When compared to the commercial Zn2SiO4:Mn2+ with a long luminescence lifetime of 11.9 ms, this conductive green phosphor has greater advantage for fast displays

Activin A and BMP4 Signaling Expands Potency of Mouse Embryonic Stem Cells in Serum-Free Media.

Inhibitors of Mek1/2 and Gsk3β, known as 2i, and, together with leukemia inhibitory factor, enhance the derivation of embryonic stem cells (ESCs) and promote ground-state pluripotency (2i/L-ESCs). However, recent reports show that prolonged Mek1/2 suppression impairs developmental potential of ESCs, and is rescued by serum (S/L-ESCs). Here, we show that culturing ESCs in Activin A and BMP4, and in the absence of MEK1/2 inhibitor (ABC/L medium), establishes advanced stem cells derived from ESCs (esASCs). We demonstrate that esASCs contributed to germline lineages, full-term chimeras and generated esASC-derived mice by tetraploid complementation. We show that, in contrast to 2i/L-ESCs, esASCs display distinct molecular signatures and a stable hypermethylated epigenome, which is reversible and similar to serum-cultured ESCs. Importantly, we also derived novel ASCs (blASCs) from blastocysts in ABC/L medium. Our results provide insights into the derivation of novel ESCs with DNA hypermethylation from blastocysts in chemically defined medium

Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting

Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10) is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii), but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus), suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR) associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5′ region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation

Identification of specific prognostic markers for lung squamous cell carcinoma based on tumor progression, immune infiltration, and stem index

IntroductionLung squamous cell carcinoma (LUSC) is a unique subform of nonsmall cell lung cancer (NSCLC). The lack of specific driver genes as therapeutic targets leads to worse prognoses in patients with LUSC, even with chemotherapy, radiotherapy, or immune checkpoint inhibitors. Furthermore, research on the LUSC-specific prognosis genes is lacking. This study aimed to develop a comprehensive LUSC-specific differentially expressed genes (DEGs) signature for prognosis correlated with tumor progression, immune infiltration,and stem index.MethodsRNA sequencing data for LUSC and lung adenocarcinoma (LUAD) were extracted from The Cancer Genome Atlas (TCGA) data portal, and DEGs analyses were conducted in TCGA-LUSC and TCGA-LUAD cohorts to identify specific DEGs associated with LUSC. Functional analysis and protein–protein interaction network were performed to annotate the roles of LUSC-specific DEGs and select the top 100 LUSC-specific DEGs. Univariate Cox regression and least absolute shrinkage and selection operator regression analyses were performed to select prognosis-related DEGs.ResultsOverall, 1,604 LUSC-specific DEGs were obtained, and a validated seven-gene signature was constructed comprising FGG, C3, FGA, JUN, CST3, CPSF4, and HIST1H2BH. FGG, C3, FGA, JUN, and CST3 were correlated with poor LUSC prognosis, whereas CPSF4 and HIST1H2BH were potential positive prognosis markers in patients with LUSC. Receiver operating characteristic analysis further confirmed that the genetic profile could accurately estimate the overall survival of LUSC patients. Analysis of immune infiltration demonstrated that the high risk (HR) LUSC patients exhibited accelerated tumor infiltration, relative to low risk (LR) LUSC patients. Molecular expressions of immune checkpoint genes differed significantly between the HR and LR cohorts. A ceRNA network containing 19 lncRNAs, 50 miRNAs, and 7 prognostic DEGs was constructed to demonstrate the prognostic value of novel biomarkers of LUSC-specific DEGs based on tumor progression, stemindex, and immune infiltration. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index.ConclusionOur study demonstrated the potential clinical implication of the 7- DEGs signature for prognosis prediction of LUSC patients based on tumor progression, immune infiltration, and stem index. And the FGG could be an independent prognostic biomarker of LUSC promoting cell proliferation, migration, invasion, THP-1 cell infiltration, and stem cell maintenance