HER2 Targeted Molecular MR Imaging Using a De Novo Designed Protein Contrast Agent

The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by the lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We have developed a novel MR imaging probe targeting to HER2, a biomarker for various cancer types and a drug target for anti-cancer therapies. This multimodal HER20targeted MR imaging probe integrates a de novo designed protein contrast agent with a high affinity HER2 affibody and a near IR fluorescent dye. Our probe can differentially monitor tumors with different expression levels of HER2 in both human cell lines and xenograft mice models. In addition to its 100-fold higher dose efficiency compared to clinically approved non-targeting contrast agent DTPA, our developed agent also exhibits advantages in crossing the endothelial boundary, tissue distribution, and tumor tissue retention over reported contrast agents as demonstrated by even distribution of the imaging probe across the entire tumor mass. This contrast agent will provide a powerful tool for quantitative assessment of molecular markers, and improved resolution for diagnosis, prognosis and drug discovery

QTL Detection for Kernel Size and Weight in Bread Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map

High-density genetic linkage maps are essential for precise mapping quantitative trait loci (QTL) in wheat (Triticum aestivum L.). In this study, a high-density genetic linkage map consisted of 6312 SNP and SSR markers was developed to identify QTL controlling kernel size and weight, based on a recombinant inbred line (RIL) population derived from the cross of Shixin828 and Kenong2007. Seventy-eight putative QTL for kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), and thousand kernel weight (TKW) were detected over eight environments by inclusive composite interval mapping (ICIM). Of these, six stable QTL were identified in more than four environments, including two for KL (qKL-2D and qKL-6B.2), one for KW (qKW-2D.1), one for KDR (qKDR-2D.1) and two for TKW (qTKW-5A and qTKW-5B.2). Unconditional and multivariable conditional QTL mapping for TKW with respect to TKW component (TKWC) revealed that kernel dimensions played an important role in regulating the kernel weight. Seven QTL-rich genetic regions including seventeen QTL were found on chromosomes 1A (2), 2D, 3A, 4B and 5B (2) exhibiting pleiotropic effects. In particular, clusters on chromosomes 2D and 5B possessing significant QTL for kernel-related traits were highlighted. Markers tightly linked to these QTL or clusters will eventually facilitate further studies for fine mapping, candidate gene discovery and marker-assisted selection (MAS) in wheat breeding

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

Morphological diversity of single neurons in molecularly defined cell types.

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits

Low-thermal remediation of mercury-contaminated soil and cultivation of treated soil

In this study, low-thermal technology was used to treat the mercury contaminated farmland soil from a chemical plant in Guizhou Province, China. A series of field planting experiments were also aimed at determining the content of total and methyl-Hg in crop plants after thermal treatment. The results showed that the mercury concentration in soils was reduced about 70% from 255.74 mg/kg to 80.63 mg/kg when treated at 350 A degrees C for 30 min in engineering-scale experiments, and the treated soil retained most of its original soil. Organic-bound and residual mercury in treated soil were reduced by 64.1 and 56.4% by means of a sequential extraction procedure, respectively. The total and methyl-mercury concentrations in crops decreased significantly, and the degree of soil mercury accumulation to crop roots has been reduced significantly. The total Hg concentrations in potato and corn were lower than the mercury tolerance limits for food in China, and the Hg concentration of radish was close to the limit. The technology provides a more sustainable remediation method for treating mercury-contaminated farmland soil in future engineering applications

Anisotropic nanocrystalline SmCo4.8Cr0.12C0.08 permanent magnets fabricated using melt-spinning method

Anisotropic CaCu5-type SmCo4.8Cr0.12C0.08 alloys with a dendritic nanostructure and an out-of-plane texture were fabricated using the melt-spinning method at a speed of 50 m/s. The microstructure changed from randomly orientated equiaxial grains for the ribbon melt-spun at 30 m/s to dendritic ones for that spun at 50 m/s. High-angle annular dark-field scanning transmission electron microscopy and X-ray energy dispersive spectroscopy analysis reveal that the distribution of carbon in SmCo5 grains obtained at higher speeds is highly inhomogeneous and leads to the formation of C-depleted and C-rich dendrite structure with a [0001](C-richSmCo5) broken vertical bar broken vertical bar [0001](C-depleted SmCo5) orientation relationship. Moreover, the incorporation of C into the SmCo5 phase helps to increase the Curie temperature to about 845 degrees C. A high coercivity of 40.3 kOe and a relatively high remanence of 42.0 emu/g were measured in the direction normal to the ribbon plane. (C) 2017 Elsevier B.V. All rights reserved

Axonopus compressus (Sw.) Beauv. : a potential biomonitor for molybdenum in soil pollution

Phytoremediation is an emerging technology that utilizes plants to remediate contaminated environments. In this study, Axonopus compressus (Sw.) Beauv, a fast-growing and hardy groundcover with wide geographical distribution, was exposed to soil Mo treatments ranging from 100 to 1000 mg/kg under tropical greenhouse conditions for five weeks. Generally, Mo accumulation increased as the concentration of Mo in the soil increased. The species was found to accumulate about 4000 mg/kg of Mo without exhibiting severe physiological stress at 600 mg/kg of soil Mo. Maximum accumulation of 6000 mg/kg Mo was observed at the 1000 mg/kg soil Mo treatment, though with severe necrosis and eventual plant mortality. The physiological observations, Mo accumulation behavior, and a bioconcentration factor of about 1 indicated that A. compressus could be a potential biomonitor of Mo.The authors thank Jurong Town Corporation (JTC), Singapore, for providing the grant to support this research study. They also express gratitude to Chua Jit Chern, Boo Chih Min, and Uvaria Tide (Singapore) for their support and expertise on plants. They declare that they have no competing interests

Characterization of photocatalytic TiO2 powder under varied environments using near ambient pressure X-ray photoelectron spectroscopy.

Consecutive eight study phases under the successive presence and absence of UV irradiation, water vapor, and oxygen were conducted to characterize surface changes in the photocatalytic TiO2 powder using near-ambient-pressure X-ray photoelectron spectroscopy (XPS). Both Ti 2p and O 1s spectra show hysteresis through the experimental course. Under all the study environments, the bridging hydroxyl (OHbr) and terminal hydroxyl (OHt) are identified at 1.1-1.3 eV and 2.1-2.3 eV above lattice oxygen, respectively. This enables novel and complementary approach to characterize reactivity of TiO2 powder. The dynamic behavior of surface-bound water molecules under each study environment is identified, while maintaining a constant distance of 1.3 eV from the position of water vapor. In the dark, the continual supply of both water vapor and oxygen is the key factor retaining the activated state of the TiO2 powder for a time period. Two new surface peaks at 1.7-1.8 and 4.0-4.2 eV above lattice oxygen are designated as peroxides (OOH/H2O2) and H2O2 dissolved in water, respectively. The persistent peroxides on the powder further explain previously observed prolonged oxidation capability of TiO2 powder without light irradiation

Characterization of photocatalytic TiO2 powder under varied environments using near ambient pressure X-ray photoelectron spectroscopy.

Consecutive eight study phases under the successive presence and absence of UV irradiation, water vapor, and oxygen were conducted to characterize surface changes in the photocatalytic TiO2 powder using near-ambient-pressure X-ray photoelectron spectroscopy (XPS). Both Ti 2p and O 1s spectra show hysteresis through the experimental course. Under all the study environments, the bridging hydroxyl (OHbr) and terminal hydroxyl (OHt) are identified at 1.1-1.3 eV and 2.1-2.3 eV above lattice oxygen, respectively. This enables novel and complementary approach to characterize reactivity of TiO2 powder. The dynamic behavior of surface-bound water molecules under each study environment is identified, while maintaining a constant distance of 1.3 eV from the position of water vapor. In the dark, the continual supply of both water vapor and oxygen is the key factor retaining the activated state of the TiO2 powder for a time period. Two new surface peaks at 1.7-1.8 and 4.0-4.2 eV above lattice oxygen are designated as peroxides (OOH/H2O2) and H2O2 dissolved in water, respectively. The persistent peroxides on the powder further explain previously observed prolonged oxidation capability of TiO2 powder without light irradiation