Engineering topics

Chen, Feng

Publications and source records attributed to Chen, Feng.

At least 73 records · Page 4

DOE OSTI2017

Nonequilibrium diagrammatic technique for Hubbard Green functions

Here, we introduce diagrammatic technique for Hubbard nonequilibrium Green functions. The formulation is an extension of equilibrium considerations for strongly correlated lattice models to description of current carrying molecular junctions. Within the technique intra-system interactions are taken into account exactly, while molecular coupling to contacts is used as a small parameter in perturbative expansion. We demonstrate the viability of the approach with numerical simulations for a generic junction model of quantum dot coupled to two electron reservoirs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Intrinsic and Stable Conjugation of Thiolated Mesoporous Silica Nanoparticles with Radioarsenic

The development of new image-guided drug delivery tools to improve the therapeutic efficacy of chemotherapeutics remains an important goal in nanomedicine. Using labeling strategies that involve radioelements that have theranostic pairs of diagnostic positron-emitting isotopes and therapeutic electron-emitting isotopes has promise in achieving this goal and further enhancing drug performance through radiotherapeutic effects. The isotopes of radioarsenic offer such theranostic potential and would allow for the use of positron emission tomography (PET) for image-guided drug delivery studies of the arsenic-based chemotherapeutic arsenic trioxide (ATO). Thiolated mesoporous silica nanoparticles (MSN) are shown to effectively and stably bind cyclotron-produced radioarsenic. Labeling studies elucidate that this affinity is a result of specific binding between trivalent arsenic and nanoparticle thiol surface modification. Serial PET imaging of the in vivo murine biodistribution of radiolabeled silica nanoparticles shows very good stability toward dearsenylation that is directly proportional to silica porosity. Thiolated MSNs are found to have a macroscopic arsenic loading capacity of 20 mg of ATO per gram of MSN, sufficient for delivery of chemotherapeutic quantities of the drug. In conclusion, these results show the great potential of radioarsenic-labeled thiolated MSN for the preparation of theranostic radiopharmaceuticals and image-guided drug delivery of ATO-based chemotherapeutics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2016

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Long-range barcode labeling-sequencing

Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Highly Efficient Luminescent Metal–Organic Framework for the Simultaneous Detection and Removal of Heavy Metals from Water

For this work, we have designed and synthesized an isoreticular series of luminescent metal-organic frameworks (LMOFs) by incorporating a strongly emissive molecular fluorophore and functionally diverse colinkers into Zn-based structures. The three-dimensional porous networks of LMOF-261, -262, and -263 represent a unique/new type of nets, classified as a 2-nodal, (4,4)-c net (mot-e type) with 4-fold, class IIIa interpenetration. All compounds crystallize in a body-centered tetragonal crystal system (space group I4 1 /a). A systematic study has been implemented to analyze their interactions with heavy metals. LMOF-263 exhibits impressive water stability, high porosity, and strong luminescence, making it an excellent candidate as a fluorescent chemical sensor and adsorbent for aqueous contaminants. It is extremely responsive to toxic heavy metals at a parts per billion level (3.3 ppb Hg 2+ , 19.7 ppb Pb 2+ ) and demonstrates high selectivity for heavy metals over light metals, with detection ratios of 167.4 and 209.5 for Hg 2+ /Ca 2+ and Hg 2+ /Mg 2+ , respectively. Mixed-metal adsorption experiments also show that LMOF-263 selectively adsorbs Hg 2+ over other heavy metal ions in addition to light metals. The Pb 2+ K SV value for LMOF-263 (55,017 M -1 ) is the highest among LMOFs reported to date, and the Hg 2+ K SV value is the second highest (459,446 M -1 ). LMOF-263 exhibits a maximum adsorption capacity of 380 mg Hg 2+ /g. The Hg 2+ adsorption process follows pseudo-second-order kinetics, removing 99.1% of the metal within 30 min. An in situ XPS study provides insight to help understand the interaction mechanism between Hg 2+ and LMOF-263. No other MOFs have demonstrated such a high performance in both the detection and the capture of Hg 2+ from aqueous solution.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants

Here, the vast abundance of terpene natural products in nature is due to enzymes known as terpene synthases (TPSs) that convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic carbon skeletons. Yet the evolution of TPSs is not well understood at higher levels of classification. Microbial TPSs from bacteria and fungi are only distantly related to typical plant TPSs, whereas genes similar to microbial TPS genes have been recently identified in the lycophyte Selaginella moellendorffii . The goal of this study was to investigate the distribution, evolution, and biochemical functions of microbial terpene synthase-like ( MTPSL ) genes in other plants. By analyzing the transcriptomes of 1,103 plant species ranging from green algae to flowering plants, putative MTPSL genes were identified predominantly from nonseed plants, including liverworts, mosses, hornworts, lycophytes, and monilophytes. Directed searching for MTPSL genes in the sequenced genomes of a wide range of seed plants confirmed their general absence in this group. Among themselves, MTPSL proteins from nonseed plants form four major groups, with two of these more closely related to bacterial TPSs and the other two to fungal TPSs. Two of the four groups contain a canonical aspartate-rich “DDxxD” motif. The third group has a “DDxxxD” motif, and the fourth group has only the first two “DD” conserved in this motif. Upon heterologous expression, representative members from each of the four groups displayed diverse catalytic functions as monoterpene and sesquiterpene synthases, suggesting these are important for terpene formation in nonseed plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Synchrotron FTIR microspectroscopy reveals early adipogenic differentiation of human mesenchymal stem cells at single-cell level

Human mesenchymal stem cells (hMSCs) have been used as an ideal in vitro model to study human adipogenesis. However, little knowledge of the early stage differentiation greatly hinders our understanding on the mechanism of the adipogenesis processes. In this study, synchrotron radiation-based Fourier transform infrared (SR-FTIR) microspectroscopy was applied to track the global structural and compositional changes of lipids, proteins and nucleic acids inside individual hMSCs along the time course. The multivariate analysis of the SR-FTIR spectra distinguished the dynamic and significant changes of the lipids and nucleic acid at early differentiation stage. Importantly, changes of lipid structure during early days (Day 1–3) of differentiation might serve as a potential biomarker in identifying the state in early differentiation at single cell level. These results proved that SR-FTIR is a powerful tool to study the stem cell fate determination and early lipogenesis events. - Highlights: • Molecular events occur in the early adipogenic differentiation stage of hMSCs are studied by SR-FTIR. • SR-FTIR data suggest that lipids may play an important role in hMSCs determination. • As potential biomarkers, lipids peaks can identify the state of cell in early differentiation stage at single-cell level.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

Research toward renewable and sustainable energy has identified candidate terpenes capable of blending/replacing petroleum-derived jet, diesel and tactical fuels. Additionally, despite being naturally produced and stored by many plants, there are few examples of commercial recovery of terpenes from plants due to low yields. Plant terpene biosynthesis is regulated at multiple levels leading to wide variability in terpene content and chemistry. Advances in the plant molecular toolkit including annotated genomes, high-throughput omics profiling and genome-editing provides an ideal platform for high-resolution analysis and in-depth understanding of plant terpene metabolism. Concomitantly, such information is useful for bioengineering strategies of metabolic pathways for candidate terpenes. Within this paper, we review the status of terpenes as an advanced biofuel and discuss the potential of plants as a viable agronomic solution for future advanced terpene-derived biofuels.

09 BIOMASS FUELS↗

DOE OSTI2016

Molecular characterization, phylogeny analysis and pathogenicity of a Muscovy duck adenovirus strain isolated in China in 2014

This study aimed to characterize a novel adenovirus (AdV) isolated from diseased Muscovy ducks in China. After the AdV was successfully propagated in duck embryo fibroblasts, the morphological and physicochemical properties of the virions were studied by electron microscopy and different tests. The results of the analyses were in conformity with AdV properties. The full genome sequence was determined and analyzed. The new isolate (named CH-GD-12-2014) shared over 91% sequence identity with duck AdV-2 representing the species Duck aviadenovirus B. The most important distinguishing feature between the two DAdV strains was the presence of a second fiber gene in the Chinese isolate. Phylogeny reconstruction confirmed the affiliation of the virus with goose and duck AdVs in the genus Aviadenovirus. Experimental infection resulted in embryo death, and intramuscular inoculation provoked morbidity and mortality among ducks and chickens. - Highlights: • A duck adenovirus type 3 was isolated and the complete genome of DAdV-3 was obtained. • Physicochemical properties and electron microscopy were researched. • Pathogenicity of duck adenovirus type 3 was researched.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycines

Soybean ( Glycine max (L.) Merr.) salicylic acid methyl transferase (GmSAMT1) catalyses the conversion of salicylic acid to methyl salicylate. Prior results showed that when GmSAMT1 was overexpressed in transgenic soybean hairy roots, resistance is conferred against soybean cyst nematode (SCN), Heterodera glycines Ichinohe. In this study, we produced transgenic soybean overexpressing GmSAMT1 and characterized their response to various SCN races. Transgenic plants conferred a significant reduction in the development of SCN HG type 1.2.5.7 (race 2), HG type 0 (race 3) and HG type 2.5.7 (race 5). Among transgenic lines, GmSAMT1 expression in roots was positively associated with SCN resistance. In some transgenic lines, there was a significant decrease in salicylic acid titer relative to control plants. No significant seed yield differences were observed between transgenics and control soybean plants grown in one greenhouse with 22 °C day/night temperature, whereas transgenic soybean had higher yield than controls grown a warmer greenhouse (27 °C day/23 °C night) temperature. In a 1-year field experiment in Knoxville, TN, there was no significant difference in seed yield between the transgenic and nontransgenic soybean under conditions with negligible SCN infection. We hypothesize that GmSAMT1 expression affects salicylic acid biosynthesis, which, in turn, attenuates SCN development, without negative consequences to soybean yield or other morphological traits. Furthermore, we conclude that GmSAMT1 overexpression confers broad resistance to multiple SCN races, which would be potentially applicable to commercial production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

A possible new origin of long absorption tail in Nd-doped yttrium aluminum garnet induced by 15 MeV gold-ion irradiation and heat treatment

When ion irradiation introduces point-defects in semiconductors/insulators, discrete energy levels can be introduced in the bandgap, and then optical transitions whose energies are lower than the bandgap become possible. The electronic transitions between the discrete level and the continuous host band are observed as a continuous tail starting from the fundamental edge. This is the well-known mechanism of the absorption tail close to the band-edge observed in many semiconductors/insulators. In this paper, we propose another mechanism for the absorption tail, which is probably active in Nd-doped yttrium aluminum garnet (Nd:YAG) after ion irradiation and annealing. A Nd:YAG bulk crystal was irradiated with 15 MeV Au{sup 5+} ions to a fluence of 8 × 10{sup 14} ions/cm{sup 2}. The irradiation generates an amorphous layer of ∼3 μm thick with refractive index reduction of Δn = −0.03. Thermal annealing at 1000 °C induces recrystallization to randomly aligned small crystalline grains. Simultaneously, an extraordinarily long absorption tail appeared in the optical spectrum covering from 0.24 to ∼2 μm without fringes. The origin of the tail is discussed based on two models: (i) conventional electronic transitions between defect levels and YAG host band and (ii) enhanced light scattering by randomly aligned small grains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

BIDIRECTIONAL OUTFLOWS AS EVIDENCE OF MAGNETIC RECONNECTION LEADING TO A SOLAR MICROFLARE

Magnetic reconnection is a rapid energy release process that is believed to be responsible for flares on the Sun and stars. Nevertheless, such flare-related reconnection is mostly detected to occur in the corona, while there have been few studies concerning the reconnection in the chromosphere or photosphere. Here, we present both spectroscopic and imaging observations of magnetic reconnection in the chromosphere leading to a microflare. During the flare peak time, chromospheric line profiles show significant blueshifted/redshifted components on the two sides of the flaring site, corresponding to upflows and downflows with velocities of ±(70–80) km s{sup −1}, comparable with the local Alfvén speed as expected by the reconnection in the chromosphere. The three-dimensional nonlinear force-free field configuration further discloses twisted field lines (a flux rope) at a low altitude, cospatial with the dark threads in He i 10830 Å images. The instability of the flux rope may initiate the flare-related reconnection. These observations provide clear evidence of magnetic reconnection in the chromosphere and show the similar mechanisms of a microflare to those of major flares.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

High Yield Production and Radiochemical Isolation of Isotopically Pure Arsenic-72 and Novel Radioarsenic Labeling Strategies for the Development of Theranostic Radiopharmaceuticals

Radioisotopes of arsenic are of considerable interest to the field of nuclear medicine with unique nuclear and chemical properties making them well-suited for use in novel theranostic radiopharmaceuticals. However, progress must still be made in the production of isotopically pure radioarsenic and in its stable conjugation to biological targeting vectors. This work presents the production and irradiation of isotopically enriched 72 Ge(m) discs in an irrigation-cooled target system allowing for the production of isotopically pure 72 As with capability on the order of 10 GBq. A radiochemical separation procedure isolated the reactive trivalent radioarsenic in a small volume buffered aqueous solution, while reclaiming 72 Ge target material. The direct thiol-labeling of a monoclonal antibody resulted in a conjugate exhibiting exceptionally poor in vivo stability in a mouse model. This prompted further investigations to alternative radioarsenic labeling strategies, including the labeling of the dithiol-containing chelator dihydrolipoic acid, and thiol-modified mesoporous silica nanoparticles (MSN-SH). In conclusion, radioarsenic-labeled MSN-SH showed exceptional in vivo stability toward dearsenylation.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2015

SELF-ABSORPTION IN THE SOLAR TRANSITION REGION

Transient brightenings in the transition region of the Sun have been studied for decades and are usually related to magnetic reconnection. Recently, absorption features due to chromospheric lines have been identified in transition region emission lines raising the question of the thermal stratification during such reconnection events. We analyze data from the Interface Region Imaging Spectrograph in an emerging active region. Here the spectral profiles show clear self-absorption features in the transition region lines of Si iv. While some indications existed that opacity effects might play some role in strong transition region lines, self-absorption has not been observed before. We show why previous instruments could not observe such self-absorption features, and discuss some implications of this observation for the corresponding structure of reconnection events in the atmosphere. Based on this we speculate that a range of phenomena, such as explosive events, blinkers or Ellerman bombs, are just different aspects of the same reconnection event occurring at different heights in the atmosphere.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Surface and Structural Investigation of a MnO x Birnessite‐Type Water Oxidation Catalyst Formed under Photocatalytic Conditions

Abstract Catalytically active MnO x species have been reported to form in situ from various Mn‐complexes during electrocatalytic and solution‐based water oxidation when employing cerium(IV) ammonium ammonium nitrate (CAN) oxidant as a sacrificial reagent. The full structural characterization of these oxides may be complicated by the presence of support material and lack of a pure bulk phase. For the first time, we show that highly active MnO x catalysts form without supports in situ under photocatalytic conditions. Our most active 4 MnO x catalyst (∼0.84 mmol O 2 mol Mn −1 s −1 ) forms from a Mn 4 O 4 bearing a metal–organic framework. 4 MnO x is characterized by pair distribution function analysis (PDF), Raman spectroscopy, and HR‐TEM as a disordered, layered Mn‐oxide with high surface area (216 m 2 g −1 ) and small regions of crystallinity and layer flexibility. In contrast, the S MnO x formed from Mn 2+ salt gives an amorphous species of lower surface area (80 m 2 g −1 ) and lower activity (∼0.15 mmol O 2 mol Mn −1 s −1 ). We compare these catalysts to crystalline hexagonal birnessite, which activates under the same conditions. Full deconvolution of the XPS Mn2p 3/2 core levels detects enriched Mn 3+ and Mn 2+ content on the surfaces, which indicates possible disproportionation/comproportionation surface equilibria.

Deibert, Benjamin J.↗

DOE OSTI2015

Substrate-Assisted Catalysis in the Reaction Catalyzed by Salicylic Acid Binding Protein 2 (SABP2), a Potential Mechanism of Substrate Discrimination for Some Promiscuous Enzymes

Although one of an enzyme’s hallmarks is the high specificity for their natural substrates, substrate promiscuity has been reported more frequently. We know that promiscuous enzymes generally show different catalytic efficiencies to different substrates, but our understanding of the origin of such differences is still lacking. We report the results of quantum mechanical/molecular mechanical simulations and an experimental study of salicylic acid binding protein 2 (SABP2). SABP2 has promiscuous esterase activity toward a series of substrates but shows a high activity toward its natural substrate, methyl salicylate (MeSA). Finally, our results demonstrate that this enzyme may use substrate-assisted catalysis involving the hydroxyl group from MeSA to enhance the activity and achieve substrate discrimination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Primer and platform effects on 16S rRNA tag sequencing

Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data produced with different protocols can be meaningfully compared, is often unknown. Here we compare results obtained using three different amplification primer sets (targeting V4, V6–V8, and V7–V8) and two sequencing technologies (454 pyrosequencing and Illumina MiSeq) using DNA from a mock community containing a known number of species as well as complex environmental samples whose PCR-independent profiles were estimated using shotgun sequencing. We find that paired-end MiSeq reads produce higher quality data and enabled the use of more aggressive quality control parameters over 454, resulting in a higher retention rate of high quality reads for downstream data analysis. While primer choice considerably influences quantitative abundance estimations, sequencing platform has relatively minor effects when matched primers are used. In conclusion, beta diversity metrics are surprisingly robust to both primer and sequencing platform biases.

16S rRNA gene sequencing↗

DOE OSTI2015

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a longread sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.

59 BASIC BIOLOGICAL SCIENCES↗