Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa

<p>Abstract</p> <p>Background</p> <p>In view of the immense value of <it>Brassica rapa </it>in the fields of agriculture and molecular biology, the multinational <it>Brassica rapa </it>Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial <it>B. rapa </it>linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromosomes of <it>B. rapa</it>. Consequently, the BrGSP assigned each of the linkage groups to the project members as chromosome substitutes for sequencing.</p> <p>Results</p> <p>We identified simple sequence repeat (SSR) motifs in the <it>B. rapa </it>genome with the sequences of seed BACs used for the BrGSP. By testing 749 amplicons containing SSR motifs, we identified polymorphisms that enabled the anchoring of 188 BACs onto the <it>B. rapa </it>reference linkage map consisting of 719 loci in the 10 linkage groups with an average distance of 1.6 cM between adjacent loci. The anchored BAC sequences enabled the identification of 30 blocks of conserved synteny, totaling 534.9 cM in length, between the genomes of <it>B. rapa </it>and <it>Arabidopsis thaliana</it>. Most of these were consistent with previously reported duplication and rearrangement events that differentiate these genomes. However, we were able to identify the collinear regions for seven additional previously uncharacterized sections of the A genome. Integration of the linkage map with the <it>B. rapa </it>cytogenetic map was accomplished by FISH with probes representing 20 BAC clones, along with probes for rDNA and centromeric repeat sequences. This integration enabled unambiguous alignment and orientation of the maps representing the 10 <it>B. rapa </it>chromosomes.</p> <p>Conclusion</p> <p>We developed a second generation reference linkage map for <it>B. rapa</it>, which was aligned unambiguously to the <it>B. rapa </it>cytogenetic map. Furthermore, using our data, we confirmed and extended the comparative genome analysis between <it>B. rapa </it>and <it>A. thaliana</it>. This work will serve as a basis for integrating the genetic, physical, and chromosome maps of the BrGSP, as well as for studies on polyploidization, speciation, and genome duplication in the genus <it>Brassica</it>.</p

Laccase-catalyzed cross-linking of BSA mediated by tyrosine

Tyrosine was explored as a cross-linking agent to form cross-linked bovine serum albumin (BSA) using laccase as a catalyst. Liquid chromatography-mass spectrometry (LC-MS) and fluorescence spectra indicated that tyrosine can be mainly oxidized to be dityrosine. Spectra analysis and molecular weight were used to characterize the BSA treated with tyrosine and laccase. Both SDS-PAGE and size exclusion chromatography confirmed the formation of cross-linked BSA, while most of the protein products existed as BSA–tyrosine conjugates. The MALDI-TOF analysis revealed that five tyrosine units were grafted on one BSA monomer, however one cross-linked BSA consists of two BSA monomers and 18 tyrosine. Furthermore, the content of the amino acid of BSA was identified using amino acid analysis, among those the percentage of lysine presented a visible decline from 12.36% to 11.43%, corresponding to 4-5 lysine residues. The pure and modified BSA were hydrolyzed by trypsin and the corresponding peptides were obtained. Different mass of five peptides from LC-MS spectra after hydrolysis indicated that tyrosine could react with Lys-136, Lys-204, Lys-224, Lys-322 and Lys-537 in BSA, promoting the formation of BSA–tyrosine conjugates and cross-linked BSA.This study was supported by Chinese Government Scholarship under China Scholar Council (NO. 201906790043) and “the Fundamental Research Funds for the Central Universities (NO. JUSRP52007A). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte

Magnetic structures of the Eu and Cr moments in EuCr2_{2} As2_{2} : Neutron diffraction study

The magnetic structures of the Eu2+ and Cr2+ moments in the nonsuperconducting parent compound EuCr2As2 have been determined by using neutron diffraction. While the Eu2+ moments order ferromagnetically with moments along the c direction at TC=21.0(1) K, the ordering temperature of the Cr2+ moments is found to be at very high temperature of 680(40) K by using magnetization measurements. The Cr2+ moments order in a G-type antiferromagnetic structure with moments along the c direction. According to this magnetic structure, the nearest-neighbor Cr2+ moments are antiferromagnetically aligned in the a−b plane as well as in the c direction. The ordered magnetic moment of the Eu2+ and Cr2+ amounts to 6.2(5)μB and 1.7(4)μB, respectively, at T=2 K

Fenton reagent reduces the level of arsenic in paddy rice grain

Hydroponic and pot experiments were conducted to examine the effects of Fenton reagent on paddy rice plant growing in arsenic-contaminated soils. Fenton reagent significantly reduced arsenic phytotoxicity, uptake by the plants and accumulation in rice grain. This is attributed to oxidation of As3+ to As5+ by hydroxyl radicals and immobilization of arsenate by reacting with precipitating Fe3+ to form practically insoluble compounds. Although this process enhanced the formation of Fe-enriched coatings on root surface, it appears that root plaque had limited effects on inhibiting As uptake since most of the young roots were not covered by iron plaque. It is more likely that As immobilization in the bulk soils play a major role in reducing As flux towards rhizosphere. The findings have implications for understanding As behavior in paddy field receiving rainwater-borne hydrogen peroxide and developing cost-effective techniques for reducing As level in rice grain produced from As-contaminated soil

Reduced levels of hydroxylated, polyunsaturated ultra long-chain fatty acids in the serum of colorectal cancer patients: implications for early screening and detection

<p>Abstract</p> <p>Background</p> <p>There are currently no accurate serum markers for detecting early risk of colorectal cancer (CRC). We therefore developed a non-targeted metabolomics technology to analyse the serum of pre-treatment CRC patients in order to discover putative metabolic markers associated with CRC. Using tandem-mass spectrometry (MS/MS) high throughput MS technology we evaluated the utility of selected markers and this technology for discriminating between CRC and healthy subjects.</p> <p>Methods</p> <p>Biomarker discovery was performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Comprehensive metabolic profiles of CRC patients and controls from three independent populations from different continents (USA and Japan; total <it>n </it>= 222) were obtained and the best inter-study biomarkers determined. The structural characterization of these and related markers was performed using liquid chromatography (LC) MS/MS and nuclear magnetic resonance technologies. Clinical utility evaluations were performed using a targeted high-throughput triple-quadrupole multiple reaction monitoring (TQ-MRM) method for three biomarkers in two further independent populations from the USA and Japan (total <it>n </it>= 220).</p> <p>Results</p> <p>Comprehensive metabolomic analyses revealed significantly reduced levels of 28-36 carbon-containing hydroxylated polyunsaturated ultra long-chain fatty-acids in all three independent cohorts of CRC patient samples relative to controls. Structure elucidation studies on the C28 molecules revealed two families harbouring specifically two or three hydroxyl substitutions and varying degrees of unsaturation. The TQ-MRM method successfully validated the FTICR-MS results in two further independent studies. In total, biomarkers in five independent populations across two continental regions were evaluated (three populations by FTICR-MS and two by TQ-MRM). The resultant receiver-operator characteristic curve AUCs ranged from 0.85 to 0.98 (average = 0.91 ± 0.04).</p> <p>Conclusions</p> <p>A novel comprehensive metabolomics technology was used to identify a systemic metabolic dysregulation comprising previously unknown hydroxylated polyunsaturated ultra-long chain fatty acid metabolites in CRC patients. These metabolites are easily measurable in serum and a decrease in their concentration appears to be highly sensitive and specific for the presence of CRC, regardless of ethnic or geographic background. The measurement of these metabolites may represent an additional tool for the early detection and screening of CRC.</p

Embracing open innovation to acquire external ideas and technologies and to transfer internal ideas and technologies outside

The objective of this dissertation is to increase understanding of how organizations can embrace open innovation in order to acquire external ideas and technologies from outside the organization, and to transfer internal ideas and technologies to outside the organization. The objective encompasses six sub-objectives, each addressed in one or more substudies. Altogether, the dissertation consists of nine substudies and a compendium summarizing the substudies. An extensive literature review was conducted on open innovation and crowdsourcing literature (substudies 1–4). In the subsequent empirical substudies, both qualitative research methods (substudies 5–7) and quantitative research methods (substudies 8–9) were applied. The four literature review substudies provided insights on the body of knowledge on open innovation and crowdsourcing. These substudies unveiled most of the influential articles, authors, and journals of open innovation and crowdsourcing disciplines. Moreover, they identified research gaps in the current literature. The empirical substudies offer several insightful findings. Substudy 5 shows how non-core ideas and technologies of a large firm can become valuable, especially for small firms. Intermediary platforms can find solutions to many pressing problems of large organizations by engaging renowned scientists from all over world (substudy 6). Intermediary platforms can also bring breakthrough innovations with novel mechanisms (substudy 7). Large firms are not only able to garner ideas by engaging their customers through crowdsourcing but they can also build long-lasting relations with their customers (substudies 8 and 9). Embracing open innovation brings challenges for firms too. Firms need to change their organizational structures in order to be able to fully benefit from open innovation. When crowdsourcing is successful, it produces a very large number of new ideas. This has the consequence that firms need to allocate a significant amount of resources in order to identify the most promising ideas. In an idea contest, customarily, only one or a few best ideas are rewarded (substudy 7). Sometimes, no reward is provided for the selected idea (substudies 8 and 9). Most of the ideas that are received are not implemented in practice

Farm Area Segmentation in Satellite Images Using DeepLabv3+ Neural Networks

Farm detection using low resolution satellite images is an important part of digital agriculture applications such as crop yield monitoring. However, it has not received enough attention compared to high-resolution images. Although high resolution images are more efficient for detection of land cover components, the analysis of low-resolution images are yet important due to the low-resolution repositories of the past satellite images used for timeseries analysis, free availability and economic concerns. In this paper, semantic segmentation of farm areas is addressed using low resolution satellite images. The segmentation is performed in two stages; First, local patches or Regions of Interest (ROI) that include farm areas are detected. Next, deep semantic segmentation strategies are employed to detect the farm pixels. For patch classification, two previously developed local patch classification strategies are employed; a two-step semi-supervised methodology using hand-crafted features and Support Vector Machine (SVM) modelling and transfer learning using the pretrained Convolutional Neural Networks (CNNs). For the latter, the high-level features learnt from the massive filter banks of deep Visual Geometry Group Network (VGG-16) are utilized. After classifying the image patches that contain farm areas, the DeepLabv3+ model is used for semantic segmentation of farm pixels. Four different pretrained networks, resnet18, resnet50, resnet101 and mobilenetv2, are used to transfer their learnt features for the new farm segmentation problem. The first step results show the superiority of the transfer learning compared to hand-crafted features for classification of patches. The second step results show that the model trained based on resnet50 achieved the highest semantic segmentation accuracy.acceptedVersionPeer reviewe