Intercomparison of Same-Day Remote Sensing Data for Measuring Winter Cover Crop Biophysical Traits

Winter cover crops are planted during the fall to reduce nitrogen losses and soil erosion and improve soil health. Accurate estimations of winter cover crop performance and biophysical traits including biomass and fractional vegetative groundcover support accurate assessment of environmental benefits. We examined the comparability of measurements between ground-based and spaceborne sensors as well as between processing levels (e.g., surface vs. top-of-atmosphere reflectance) in estimating cover crop biophysical traits. This research examined the relationships between SPOT 5, Landsat 7, and WorldView-2 same-day paired satellite imagery and handheld multispectral proximal sensors on two days during the 2012-2013 winter cover crop season. We compared two processing levels from three satellites with spatially aggregated proximal data for red and green spectral bands as well as the normalized difference vegetation index (NDVI). We then compared NDVI estimated fractional green cover to in-situ photographs, and we derived cover crop biomass estimates from NDVI using existing calibration equations. We used slope and intercept contrasts to test whether estimates of biomass and fractional green cover differed statistically between sensors and processing levels. Compared to top-of-atmosphere imagery, surface reflectance imagery were more closely correlated with proximal sensors, with intercepts closer to zero, regression slopes nearer to the 1:1 line, and less variance between measured values. Additionally, surface reflectance NDVI derived from satellites showed strong agreement with passive handheld multispectral proximal sensor-sensor estimated fractional green cover and biomass (adj. R2 = 0.96 and 0.95; RMSE = 4.76% and 259 kg ha-1, respectively). Although active handheld multispectral proximal sensor-sensor derived fractional green cover and biomass estimates showed high accuracies (R2 = 0.96 and 0.96, respectively), they also demonstrated large intercept offsets (-25.5 and 4.51, respectively). Our results suggest that many passive multispectral remote sensing platforms may be used interchangeably to assess cover crop biophysical traits whereas SPOT 5 required an adjustment in NDVI intercept. Active sensors may require separate calibrations or intercept correction prior to combination with passive sensor data. Although surface reflectance products were highly correlated with proximal sensors, the standardized cloud mask failed to completely capture cloud shadows in Landsat 7, which dampened the signal of NIR and red bands in shadowed pixels.

Comparing NISAR (Using Sentinel-1), USDA/NASS CDL, and Ground Truth Crop/Non-Crop Areas in an Urban Agricultural Region

A general limitation in assessing the accuracy of land cover mapping is the availability of ground truth data. At sites where ground truth is not available, potentially inaccurate proxy datasets are used for sub-field-scale resolution investigations at large spatial scales, i.e., in the Contiguous United States. The USDA/NASS Cropland Data Layer (CDL) is a popular agricultural land cover dataset due to its high accuracy (>80%), resolution (30 m), and inclusions of many land cover and crop types. However, because the CDL is derived from satellite imagery and has resulting uncertainties, comparisons to available in situ data are necessary for verifying classification performance. This study compares the cropland mapping accuracies (crop/non-crop) of an optical approach (CDL) and the radar-based crop area (CA) approach used for the upcoming NASA-ISRO Synthetic Aperture Radar (NISAR) L- and S-band mission but using Sentinel-1 C-band data. CDL and CA performance are compared to ground truth data that includes 54 agricultural production and research fields located at USDA's Beltsville Agricultural Research Center (BARC) in Maryland, USA. We also evaluate non-crop mapping accuracy using twenty-six built-up and thirteen forest sites at BARC. The results show that the CDL and CA have a good pixel-wise agreement with one another (87%). However, the CA is notably more accurate compared to ground truth data than the CDL. The 2017-2021 mean accuracies for the CDL and CA, respectively, are 77% and 96% for crop, 100% and 94% for built-up, and 100% and 100% for forest, yielding an overall accuracy of 86% for the CDL and 96% for CA. This difference mainly stems from the CDL under-detecting crop cover at BARC, especially in 2017 and 2018. We also note that annual accuracy levels varied less for the CA (91-98%) than for the CDL (79-93%). This study demonstrates that a computationally inexpensive radar-based cropland mapping approach can also give accurate results over complex landscapes with accuracies similar to or better than optical approaches.

Comparison of Near-surface NO2 Pollution with Pandora Total Column NO2 during the Korea-United States Ocean Color (KORUS OC) Campaign

Near-surface air quality (AQ) observations over coastal waters are scarce, a situation that limits our capacity to monitor pollution events at land-water interfaces. Satellite measurements of total column (TC) nitrogen dioxide (NO₂) observations are a useful proxy for combustion sources but the once daily snapshots available from most sensors are insufficient for tracking the diurnal evolution and transport of pollution. Ground-based remote sensors like the Pandora Spectrometer Instrument (PSI) that have been developed to verify space-based total column NO₂ and other trace gases are being tested for routine use as certified AQ monitors. The KORUS-OC (Korea-United States Ocean Color) cruise aboard the R/V Onnuri in May-June 2016 represented an opportunity to study AQ near the South Korean coast, a region affected by both local/regional and long-distance pollution sources. Using PSI data in direct-sun mode and in situ sensors for shipboard ozone, CO and NO₂, we explore, for the first time, relationships between TC NO₂ and surface AQ in this coastal region. Three case studies illustrate the value of the PSI as well as complexities in the surface-column NO₂ relationship caused by varying meteorological conditions. Case Study 1 (25-26 May 2016) exhibited a high correlation of surface NO₂ to TC NO₂ measured by both PSI and Aura's Ozone Monitoring Instrument (OMI) but two other cases displayed poor relationships between in situ and TC NO₂ due to decoupling of pollution layers from the surface. With suitable interpretation the PSI TC NO₂ measurement demonstrates good potential for working with upcoming geostationary satellites to advance diurnal tracking of pollution.

MPIDB: the microbial protein interaction database

Summary: The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 22 530 experimentally determined interactions among proteins of 191 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 24 060 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did).

Availability:http://www.jcvi.org/mpidb/

Contact:jgoll@jcvi.org

Autophagic vacuoles are enriched in amyloid precursor protein-secretase activities: implications for β-amyloid peptide over-production and localization in Alzheimer’s disease

In Alzheimer's disease (AD), the neuropathologic hallmarks of beta-amyloid deposition and neurofibrillary degeneration are associated with early and progressive pathology of the endosomal-lysosomal system. Abnormalities of autophagy, a major pathway to lysosomes for protein and organelle turnover, include marked accumulations of autophagy-related vesicular compartments (autophagic vacuoles or AVs) in affected neurons. Here, we investigated the possibility that AVs contain the proteases and substrates necessary to cleave the amyloid precursor protein (APP) to A beta peptide that forms beta-amyloid, a key pathogenic factor in AD. AVs were highly purified using a well-established metrizamide gradient procedure from livers of transgenic YAC mice overexpressing wild-type human APP. By Western blot analysis, AVs contained APP, beta CTF - the beta-cleaved carboxyl-terminal domain of APP, and BACE, the protease-mediating beta-cleavage of APP. beta-Secretase activity measured against a fluorogenic peptide was significantly enriched in the AV fraction relative to whole-liver lysate. Compared to other recovered subcellular fractions, AVs exhibited the highest specific activity of gamma-secretase based on a fluorogenic assay and inhibition by a specific inhibitor of gamma-secretase, DAPT. AVs were also the most enriched subcellular fraction in levels of the gamma-secretase components presenilin and nicastrin. Immunoelectron microscopy demonstrated selective immunogold labeling of AVs with antibodies specific for the carboxyl termini of human A beta 40 and A beta 42. These data indicate that AVs are a previously unrecognized and potentially highly active compartment for A beta generation and suggest that the abnormal accumulation of AVs in affected neurons of the AD brain contributes to beta-amyloid deposition.

A Stable Monomeric Nickel Borohydride

A stable discrete nickel borohydride complex (Tp*NiBH(4) or Tp*NiBD(4)) was prepared using the nitrogen-donor ligand hydrotris(3,5-dimethylpyrazolyl)borate (Tp*-). This complex represents one of the best characterized nickel(II) borohydrides to date. Tp*NiBH(4) and Tp*NiBD(4) are stable toward air, boiling water, and high temperatures (mp > 230 degrees C dec). X-ray crystallographic measurements for Tp*NiBH(4) showed a six-coordinate geometry for the complex, with the nickel(II) center facially coordinated by three bridging hydrogen atoms from borohydride and a tridentate Tp(-) ligand. For Tp*NiBH(4), the empirical formula is C(15)H(26)B(2)N(6)Ni, a = 13.469(9) A, b = 7.740(1) A, c = 18.851(2) A, beta = 107.605(9) degrees, the space group is monoclinic P2(1)/c, and Z = 4. Infrared measurements confirmed the presence of bridging hydrogen atoms; both nu(B[bond]H)(terminal) and nu(B[bond]H)(bridging) are assignable and shifted relative to nu(B-D) of Tp*NiBD(4) by amounts in agreement with theory. Despite their hydrolytic stability, Tp*NiBH(4) and Tp*NiBD(4) readily reduce halocarbon substrates, leading to the complete series of Tp*NiX complexes (X = Cl, Br, I). These reactions showed a pronounced hydrogen/deuterium rate dependence (k(H)/k(D) approximately 3) and sharp isosbestic points in progressive electronic spectra. Nickel K-edge X-ray absorption spectroscopy (XAS) measurements of a hydride-rich nickel center were obtained for Tp*NiBH(4), Tp*NiBD(4), and Tp*NiCl. X-ray absorption near-edge spectroscopy results confirmed the similar six-coordinate geometries for Tp*NiBH(4) and Tp*NiBD(4). These contrasted with XAS results for the crystallographically characterized pseudotetrahedral Tp*NiCl complex. The stability of Tp*Ni-coordinated borohydride is significant given this ion's accelerated decomposition and hydrolysis in the presence of transition metals and simple metal salts.

Neuropathological characterization of mutant amyloid precursor protein yeast artificial chromosome transgenic mice

Mutations in the amyloid precursor protein (APP) gene result in elevated production and deposition of the 42 amino acid beta-amyloid (Abeta1-42) peptide and early-onset Alzheimer's disease (AD). To accurately examine the effect of the APP FAD mutations in vivo, we introduced yeast artificial chromosomes (YACs) containing the entire genomic copy of human APP harboring FAD mutations into transgenic mice. Our current results demonstrate that mutant APP YAC transgenic mice exhibit many features characteristic of human AD, including regional deposition of Abeta with preferential deposition of Abeta1-42, extensive neuritic abnormalities as evidenced by staining with APP, ubiquitin, neurofilament, and hyperphosphorylated tau antibodies, increased markers of inflammation, and the overlapping deposition of Abeta with apolipoproteins E and J. Our results also suggest that APP YAC transgenic mice possess unique pathological attributes when compared to other transgenic mouse models of AD that may reflect the experimental design of each model.

Transgenic mouse models of Alzheimer's disease

Recent advances in the understanding of the genetic basis of Alzheimer's disease have enabled the production of transgenic mouse models of the disease. Utilizing both cDNA- and genomic-based approaches, these mouse models for Alzheimer's disease have already provided valuable insights into the pathogenesis of the disease and potential therapeutic interventions.

Altered metabolism of familial Alzheimer's disease-linked amyloid precursor protein variants in yeast artificial chromosome transgenic mice

Missense mutations in the beta-amyloid precursor protein gene (APP) co-segregate with a small subset of autosomal dominant familial Alzheimer's disease (FAD) cases wherein deposition of the 39-43 amino acid beta-amyloid (A beta) peptide and neurodegeneration are principal neuropathological hallmarks. To accurately examine the effect of missense mutations on APP metabolism and A beta production in vivo, we have introduced yeast artificial chromosomes (YACs) containing the entire approximately 400 kbp human APP gene encoding APP harboring either the asparagine for lysine and leucine for methionine FAD substitution at codons 670 and 671 (APP(K670N/M671L)), the isoleucine for valine FAD substitution at codon 717 (APP(V7171)) or a combination of both substitutions into transgenic mice. We demonstrate that, relative to YAC transgenic mice expressing wild-type APP, high levels of A beta peptides are detected in the brains of YAC transgenic mice expressing human APP(K670N/M671L) that is associated with a concomitant diminution in the levels of apha-secretase-generated soluble APP derivatives. Moreover, the levels of longer A beta peptides (species terminating at amino acids 42/43) are elevated in YAC transgenic mice expressing human APP(V7171). These mice should prove valuable for detailed analysis of the in vivo effects of the APP FAD mutations in a variety of tissues and throughout aging and for testing therapeutic agents that specifically alter APP metabolism and A beta production.

Novel neuritic clusters with accumulations of amyloid precursor protein and amyloid precursor-like protein 2 immunoreactivity in brain regions damaged by thiamine deficiency

Experimental thiamine deficiency (TD) is a classical model of a nutritional deficit associated with a generalized impairment of oxidative metabolism and selective cell loss in the brain. In rats, TD-induced cell degeneration is accompanied by an accumulation of amyloid precursor protein (APP)/amyloid precursor-like protein 2 (APLP2) immunoreactivity in abnormal neurites and perikarya along the periphery of, or scattered within, the lesion. Prompted by these data and our previous findings of a genetic variation in the development of TD symptoms, we extended our studies to mice. C57BL/6, ApoE knockout, and APP YAC transgenic mice received thiamine-deficient diet and pyrithiamine injections. Unlike rats, APP/APLP2-immunoreactive neurites in all strains of mice were sparsely scattered within damaged areas and did not delimit the thalamic lesion. In addition, abnormal clusters of intensely immunoreactive neurites occurred only in areas of damage including the thalamus, mammillary body, and inferior colliculus. The clusters appeared as either irregular clumps or round or oval rosettes that strikingly resembled the neuritic component of Alzheimer amyloid plaques. However, immunostaining using various antisera to synthetic amyloid beta-protein (A beta 1-40) and thioflavine S histochemistry failed to show evidence of a component of A beta Neither APP/APLP2-immunoreactive clusters nor amyloid plaques were observed in the brain from patients with Wernicke-Korsakoff syndrome, the clinical manifestation of TD in man. Our results demonstrate species (i.e., genetic) differences in the response to TD-induced damage and support a role for APP and APLP2 in the response to brain injury. This is the first report that chronic oxidative deficits can lead to this novel pathology.

Alterations of yeast artificial chromosome transgenic sequences in stretched embryonic stem-cell chromatin visualized by fluorescence in situ hybridization

Transgenic mice have been generated from embryonic stem (ES) cells carrying functional genes cloned within yeast artificial chromosomes (YACs). Information on the integrity and organization of the inserted sequences, including the number of copies and their orientation to each other, is still limited by current methods. We have applied fluorescence in situ hybridization to stretched chromatin preparations from YAC-transfected ES cells to analyze the organization and copy number of the integrated sequences.

YAC transgenics and the study of genetics and human disease

Advances in yeast artificial chromosome (YAC) technologies over the past decade have enabled the precise identification and manipulation of large genomic regions (>100 kb) of DNA. Introduction of YACs into the mouse germline has now been accomplished through transfection of mouse embryonic stem cells as well as through pronuclear microinjection, allowing the efficient transfer defined genomic loci into mice. YAC transgenics will have a profound impact on the development of transgenic mice as bioreactors and as models of human disease, and on the functional analysis of higher order genomic structure.

Introduction and expression of the 400 kilobase amyloid precursor protein gene in transgenic mice [corrected]

Overexpression of the gene encoding the beta-amyloid precursor protein (APP) may have a key role in the pathogenesis of both Alzheimer's disease (AD) and Down Syndrome (DS). We have therefore introduced a 650 kilobase (kb) yeast artificial chromosome (YAC) that contains the entire, unrearranged 400 kb human APP gene into mouse embryonic stem (ES) cells by lipid-mediated transfection. ES lines were generated that contain a stably integrated, unrearranged human APP gene. Moreover, we demonstrate germ line transmission of the APP YAC in transgenic mice and expression of human APP mRNA and protein at levels comparable to endogenous APP. This transgenic strategy may prove invaluable for the development of mouse models for AD and DS.

A DNA element that regulates expression of an endogenous retrovirus during F9 cell differentiation is E1A dependent

The retinoic acid-induced differentiation of F9 cells into parietal endoderm-like cells activates transcription of the endogenous mouse retrovirus, the intracisternal A-particle (IAP). To investigate the elements that control IAP gene differentiation-specific expression, we used methylation interference, Southwestern (DNA-protein), and transient-transfection assays and identified the IAP-proximal enhancer (IPE) element that directs differentiation-specific expression. We find that the IPE is inactive in undifferentiated F9 cells and active in differentiated parietal endoderm-like PYS-2 cells. Three proteins of 40, 60, and 68 kDa bind to the sequence GAGTAGAC located between nucleotides -53 and -47 within the IPE. The 40- and 68-kDa proteins from both the undifferentiated and differentiated cells exhibit similar DNA-binding activities. However, the 60-kDa protein from differentiated cells has greater binding activity than that from undifferentiated cells, suggesting a role for this protein in F9 differentiation-specific expression of the IAP gene. The IAP gene is negatively regulated by the adenovirus E1A proteins, and the E1A sequence responsible for repression is located at the N terminus, between amino acids 2 and 67. The DNA sequence that is the target of E1A repression also maps to the IPE element. Colocalization of the differentiation-specific and E1A-sensitive elements to the same protein-binding site within the IPE suggests that the E1A-like activity functions in F9 cells to repress IAP gene expression. Activation of the IAP gene may result when the E1A-like activity is lost or inactivated during F9 cell differentiation, followed by binding of the 60-kDa positive regulatory protein to the enhancer element.

CpG methylation of an endogenous retroviral enhancer inhibits transcription factor binding and activity

The endogenous retrovirus, intracisternal A-particle (IAP), is expressed at unique stages during murine embryogenesis and is also activated during the in vitro differentiation of F9 cells. We have examined the DNA elements and protein factors that control IAP expression during F9 differentiation. In the present study an IAP upstream enhancer (IUE) is identified by transient transfection assays and found to be active in both undifferentiated and differentiated cells. Further analyses reveal that a ubiquitous 65 kDa protein factor, the IUE binding protein (IUEB), binds with the IUE. Site-specific methylation within the IUEB binding site strongly inhibits both IUEB binding and IUE transcriptional activity, suggesting that methylation may regulate IUE function and IAP expression.

Mouse placental 57-kDa calcium-binding protein: II. Localization of mRNA in mouse and human placentae by in situ cDNA hybridization

Using a cloned cDNA to the mouse placental calcium-binding protein (MCaBP) [Tuan and Kirwin, preceding paper], mRNA transcripts of the MCaBP have been localized in the mouse placenta by in situ cDNA-RNA hybridization. The procedure involved the use of a nonradioactive, biotinylated cDNA probe. Paraffin sections of the mouse chorioallantoic placenta were processed for in situ hybridization using a procedure modified from that of Lo [8]. The results demonstrated that MCaBP mRNA is localized specifically to the fetal trophoblast of the mouse placenta, and is expressed in a development-dependent manner. The MCaBP cDNA also hybridized strongly in situ to sections of human term placenta, giving rise to signals localized specifically to the syncytiotrophoblastic layer of the chorionic villi.