Multiplexed biomarker detection using x-ray fluorescence of composition-encoded nanoparticles

Multiple DNA and protein biomarkers have been detected based on characteristic x-ray fluorescence of a panel of metal and alloy nanoparticles, which are modified with ligands of biomarkers to create a one-to-one correspondence and immobilized on ligand-modified substrates after forming complexes with target biomarkers in three-strand or sandwich configuration. By determining the presence and concentration of nanoparticles using x-ray fluorescence, the nature and amount of biomarkers can be detected with limits of 1 nM for DNA and 1 ng/ml for protein. By combining high penetrating ability of x-rays, this method allows quantitative imaging of multiple biomarkers

Design of flexible ultrahigh-Q microcavities in diamond-based photonic crystal slabs

We design extremely flexible ultrahigh-Q diamond-based double-heterostructure photonic crystal slab cavities by modifying the refractive index of the diamond. The refractive index changes needed for ultrahigh-Q cavities with $Q ~ 10^7$, are well within what can be achieved ($\Delta n \sim 0.02$). The cavity modes have relatively small volumes $V<2 (\lambda /n)^3$, making them ideal for cavity quantum electro-dynamic applications. Importantly for realistic fabrication, our design is flexible because the range of parameters, cavity length and the index changes, that enables an ultrahigh-Q is quite broad. Furthermore as the index modification is post-processed, an efficient technique to generate cavities around defect centres is achievable, improving prospects for defect-tolerant quantum architectures.Comment: 9 pages, 4 figures (1 in colour

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

Xray enabled detection and eradication of circulating tumor cells with nanoparticles

a b s t r a c t The early detection and eradication of circulating tumor cells (CTCs) play an important role in cancer metastasis management. This paper describes a new nanoparticle-enabled technique for integrated enrichment, detection and killing of CTCs by using magnetic nanoparticles and bismuth nanoparticles, X-ray fluorescence spectrometry, and X-ray radiation. The nanoparticles are modified with tumor targeting agents and conjugated with tumor cells through folate receptors over-expressed on cancer cells. A permanent micro-magnet is used to collect CTCs suspended inside a flowing medium that contains phosphate buffered saline (PBS) or whole blood. The characteristic X-ray emissions from collected bismuth nanoparticles, upon excitation with collimated X-rays, are used to detect CTCs. Results show that the method is capable of selectively detecting CTCs at concentrations ranging from 100-100,000 cells/mL in the buffer solution, with a detection limit of $ 100 CTCs/mL. Moreover, the dose of primary X-rays can be enhanced to kill the localized CTCs by radiation induced DNA damage, with minimal invasiveness, thus making in vivo personalized CTC management possible

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

Dchs1-Fat4 regulation of osteogenic differentiation in mouse

In human, mutations of the protocadherins FAT4 and DCHS1 result in Van Maldergem syndrome, which is characterised, in part, by craniofacial abnormalities. Here, we analyse the role of Dchs1-Fat4 signalling during osteoblast differentiation in mouse. We show that Fat4 and Dchs1 mutants mimic the craniofacial phenotype of the human syndrome and that Dchs1-Fat4 signalling is essential for osteoblast differentiation. In Dchs1/Fat4 mutants, proliferation of osteoprogenitors is increased and osteoblast differentiation is delayed. We show that loss of Dchs1-Fat4 signalling is linked to increased Yap-Tead activity and that Yap is expressed and required for proliferation in osteoprogenitors. In contrast, Taz is expressed in more-committed Runx2-expressing osteoblasts, Taz does not regulate osteoblast proliferation and Taz-Tead activity is unaffected in Dchs1/Fat4 mutants. Finally, we show that Yap and Taz differentially regulate the transcriptional activity of Runx2, and that the activity of Yap-Runx2 and Taz-Runx2 complexes is altered in Dchs1/Fat4 mutant osteoblasts. In conclusion, these data identify Dchs1-Fat4 as a signalling pathway in osteoblast differentiation, reveal its crucial role within the early Runx2 progenitors, and identify distinct requirements for Yap and Taz during osteoblast differentiation

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

Nano-manipulation of diamond-based single photon sources

The ability to manipulate nano-particles at the nano-scale is critical for the development of active quantum systems. This paper presents a new technique to manipulate diamond nano-crystals at the nano-scale using a scanning electron microscope, nano-manipulator and custom tapered optical fibre probes. The manipulation of a ~ 300 nm diamond crystal, containing a single nitrogen-vacancy centre, onto the endface of an optical fibre is demonstrated. The emission properties of the single photon source post manipulation are in excellent agreement with those observed on the original substrate.Comment: 6 pages, 4 figure