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Zhou, Jie

Publications and source records attributed to Zhou, Jie.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Necromass responses to warming: A faster microbial turnover in favor of soil carbon stabilisation

Microbial byproducts and residues (hereafter ‘necromass’) potentially play the most critical role in soil organic carbon (SOC) sequestration. However, little is known about the influence of climate warming on necromass accumulation in the agroecosystem and the underlying mechanisms associated with microbial life strategies. Here, in order to address these knowledge gaps, we used amino sugars as biomarkers of microbial necromass, and investigated their variation through an 8-year trial in an agroecosystem with two warming levels (+1.6 and + 3.2 °C) compared to ambient temperature. The results showed that the lower warming level had no impact on total microbial necromass carbon. Conversely, warming the soil 3.2 °C above ambient increased total microbial necromass by 17 % and its contribution to SOC by 21.3 %, mainly by increasing fungal necromass (+19.8 %), whereas +3.2 °C warming had no impact on bacterial necromass. At the phylum level, compared with the ambient control, +3.2 °C warming induced an increase in the abundance of Proteobacteria and a decrease in both Acidobacteria and Actinobacteria, whereas in the fungal community, Ascomycota increased and Mortierellomycota decreased. This indicates that r-strategists outcompete K-strategists in warmer climates, which led to increased microbial necromass production and accumulation, as supported by the positive correlation between r-strategists and microbial necromass. Stronger microbial competition for resources also resulted in a higher biomass turnover rate, greater cell death, and greater production of microbial necromass. This was supported by the lower bacterial and fungal network complexity and trophic links under warming conditions. In addition, the necromass generated from accelerated microbial turnover further offsets warming-induced deceases in microbial biomass. Consequently, bulk SOC did not change, despite microbial necromass having a much greater response to warming than the soil C pool. Therefore, future climate warming may influence the composition and persistence of SOC during microbial degradation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Effect of Electroacupuncture at Wushu Acupoints of the Cardiopulmonary Meridian on the Autophagy in Rats with Acute Myocardial Ischemia

Wushu acupoints are the five acupoints distributed below the human elbow and knee joint. They are all located on the same meridian and divided into five categories: Jing, Ying, Shu, Jing, and He. It has been shown that electroacupuncture (EA) at Shenmen point of heart meridian can improve acute myocardial ischemia (AMI) early. However, it is still unclear if all the Wushu acupoints of the heart meridian can improve AMI. Hence, this study emphasizes Wushu acupoints of heart meridian, compares them with Wushu acupoints of lung meridian, and studies the therapeutic effect of EA at Wushu acupoints on AMI and its possible mechanism. It also discusses the specificity of the heart meridian to heart disease. The AMI model is established by ligation of the left anterior descending coronary artery. The detection methods like the physiological recorder, TTC staining, ELISA, and so forth were used to determine the ECG, myocardial infarct size, serum myocardial enzymes, and myocardial tissue-related protein expression in rats. The heart rate (HR) and ST segment along with creatine kinase (CK), creatine kinase isoenzymes (CK-MB), lactate dehydrogenase (LDH), and myocardial infarctions increased after the induction with AMI. Furthermore, the expressions of PINK1 and Parkin protein also showed an increase. However, EA at Wushu acupoints in the heart meridian can reverse the above changes, whereas EA at the lung meridian exhibits limited effect. It is depicted that the heart meridian has a relatively specific relationship with the heart in a diseased state.

Zhu, Chao↗
DOE OSTI2022

Targeting a proteolytic neoepitope on CUB domain containing protein 1 ( CDCP1 ) for RAS -driven cancers

Extracellular proteolysis is frequently dysregulated in disease and can generate proteoforms with unique neoepitopes not found in healthy tissue. Here, we demonstrate that Abs that selectively recognize a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) could enable more effective and safer treatments for solid tumors. CDCP1 is highly overexpressed in RAS-driven cancers, and its ectodomain is cleaved by extracellular proteases. Biochemical, biophysical, and structural characterization revealed that the 2 cleaved fragments of CDCP1 remain tightly associated with minimal proteolysis-induced conformational change. Using differential phage display, we generated recombinant Abs that are exquisitely selective to cleaved CDCP1 with no detectable binding to the uncleaved form. These Abs potently targeted cleaved CDCP1-expressing cancer cells as an Ab-drug conjugate, an Ab-radionuclide conjugate, and a bispecific T cell engager. In a syngeneic pancreatic tumor model, these cleaved-specific Abs showed tumor-specific localization and antitumor activity with superior safety profiles compared with a pan-CDCP1 approach. Targeting proteolytic neoepitopes could provide an orthogonal "AND" gate for improving the therapeutic index.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural, Elastic, Electronic, and Magnetic Properties of a New Full-Heusler Alloy Mn{sub 2}MgGe: First-Principles Calculations

We present the first-principles calculations of the structural, elastic, electronic, and magnetic properties for a new full-Heusler alloy Mn{sub 2}MgGe. Both L2{sub 1} and XA structures are considered for both nonmagnetic and ferromagnetic states. The results show that the XA structure in the ferromagnetic state is the energetically most favorable for the full-Heusler alloy, and exhibits ductile behavior, significant anisotropy, and robust half-metallicity. The total spin moment is 2.000 μ{sub B} per formula unit in equilibrium state, which follows the Slater-Pauling rule. The spin-up electrons are metallic, whereas the spin-down bands are semiconductor with a gap of 1.086 eV at the equilibrium lattice constant of 6.066 Å. Half-metallicity is maintained within the lattice constant range from 5.6 to 6.1 Å. Our results indicate that Mn{sub 2}MgGe is an interesting candidate in the area of spintronics.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Elucidating the nature of crystallization kinetics in Zr 46 Cu 46 Al 8 metallic glass through simultaneous WAXS/SAXS measurements

Simultaneous wide- and small-angle X-ray scattering (WAXS/SAXS) measurements were performed to investigate the low-temperature crystallization kinetics of Zr 46 Cu 46 Al 8 bulk metallic glass during isothermal annealing. Quantitative analysis of the WAXS intensity data indicated that the crystallization process was dominated by steady-state homogeneous nucleation and three-dimensional diffusion-controlled growth. This observation was corroborated by quantitative analysis of the SAXS data showing a saturation of the growth of nanoscale crystallites. Comparison of simultaneously measured WAXS and SAXS data showed evidence of composition fluctuation prior to crystallization, suggesting that the crystallization was facilitated by nanoscale phase separation which established regions of favorable compositions catalyzing crystallization. The temperature dependence of crystallization mechanisms and the resulting microstructures in metallic glass are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

The elongation factor G (EF-G)–catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Furthermore, although the mRNA also undergoes movement, codon–anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

In-situ visualizing atomic structural evolution during crystallization in ternary Zr Cu Al bulk metallic glasses

A well-designed experimental method has been presented to in-situ visualize the amorphous-to-crystalline phase transformation of two glass formers at the atomic length scale in the supercooled liquid region using a high voltage electron microscopy (HVEM). Analysis of the HVEM high-resolution images, supported by the in situ synchrotron diffraction, further confirms previous observations of distinctively different crystallization pathways in the two Zr-Cu-Al alloys. Moreover, the HVEM results illustrate that isolated distributed nanocrystals with mutual orientation easily grew up from the Zr 56 Cu 36 Al 8 , an average glass former, which follows a classical crystallization pathway; while density population poorly ordered atomic clusters with large misorientation suspended the growth in the Zr 46 Cu 46 Al 8 , a good glass former, which might follow an unusual crystallization pathway. In addition, in-situ synchrotron diffraction measurements confirm that the Zr 56 Cu 36 Al 8 alloy finally crystallized into an extended structure, in contrast, the final crystalline product of Zr 46 Cu 46 Al 8 alloy possesses a damped structure. Our study provides a detailed microscopic understanding of the crystallization behaviors in the supercooled liquids, showing that the density population nucleation site with large misorientation and the confined final crystalline structure contribute to the stability of Zr-Cu-Al supercooled liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2018

PPARγ provides anti-inflammatory and protective effects in intrahepatic cholestasis of pregnancy through NF-κB pathway

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific hepatic disorder with potentially deleterious consequences of fetuses. Although the intimate relationship between ICP and peroxisome proliferator-activated receptor γ (PPARγ) has been previously reported in physiological and pathological conditions, the detailed mechanisms in the process of intrahepatic cholestasis of pregnancy has been unclear. The aims of this study are to assess the role of PPARγ regulating the reactive oxygen species (ROS) and inflammation in the process of the ICP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Ultrathin SnS{sub 2} nanosheets as robust polysulfides immobilizers for high performance lithium-sulfur batteries

Highlights: • Ultrathin SnS{sub 2} nanosheets have large surface area and fast charge transfer properties. • Ultrathin SnS{sub 2} nanosheets can greatly improve the electrochemical properties of S/C composites for Li-S batteries. • Superior electrochemical performance of S/C-SnS{sub 2}-10 composites can be ascribed to the optimized synergistic effects between SnS{sub 2} and porous carbon. - Abstract: Ultrathin SnS{sub 2} nanosheets modified sulfur/carbon (S/C-SnS{sub 2}) composites were synthesized through a facile method by mixing sublimed sulfur, Ketjen Black and ultrathin SnS{sub 2} nanosheets. The ultrathin SnS{sub 2} nanosheets can provide remarkable binding strength, large surface area and fast charge transfer, therefore leading to favorable chemical interaction with polysulfides in Li-S batteries. Accompanied with the synergistic effects between physical confinement of porous carbon and chemical interactions of SnS{sub 2}, S/C-SnS{sub 2} composites with different mass ratio of ultrathin SnS{sub 2} nanosheets and C show much improved electrochemical properties. Among them, S/C-SnS{sub 2} composite with 10 wt% of ultrathin SnS{sub 2} nanosheets and 75 wt% of sulfur maintains superior long term cycling capacities of 800 mAh g{sup −1} at 0.5 C after 300 cycles and 540 mAh g{sup −1} at 2 C after 700 cycles.

36 MATERIALS SCIENCE↗