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1. chinaXiv:202102.00067 [pdf]

Decomposition of different crop straws and variation in straw-associated microbial communities in a peach orchard, China

ZHANG Hong; CAO Yingfei; LYU Jialong
Subjects: Geosciences >> Geography

Crop residue is a major source of soil organic matter; therefore, application of crop straw to soil contributes to the sustainable development of organic agriculture. To better understand the transformation of crop straw in orchard soils, we investigated the relationship between the characteristics of straw decomposition and functional diversity of associated microbial communities in a long-term peach orchard, China. Mesh bags, each containing 30 g of corn or bean straw, were buried at a soil depth of 20 cm in a 12-year-old peach orchard for 360 d (October 2011–October 2012). Three treatments were applied, i.e., fresh corn straw, fresh corn straw with nitrogen fertilizer (urea, 10.34 g/kg), and fresh bean straw. Changes in straw residual rate, straw water content and soil conditions were monitored after treatment. The functional diversity of straw-associated microbial communities was analyzed by the Biolog-Eco microplate assay. During the decomposition process, straw residual rates did not vary considerably from 10 d (30.4%–45.4%) to 360 d (19.0%–30.3%). Irrespective of nitrogen addition, corn straw decomposed faster than bean straw. Corn straw with nitrogen fertilizer yielded the highest average well color development (AWCD) values (1.11–1.67), followed by corn straw (1.14–1.68) and bean straw (1.18–1.62). Although the AWCD values did not differ significantly among the three treatments, substantial differences occurred across various time periods of the decomposition process (P<0.01). In terms of carbon source utilization, the dominant microbial groups fed mainly on saccharides. Hard-to-decompose substances gradually accumulated in the middle and late stages of straw decomposition. Of the six categories of carbon sources tested, the utilization rate of aromatics was the lowest with corn straw, whereas that of polymers was the lowest with bean straw. Among different treatments, straw residual rate was negatively correlated to soil available phosphorous, soil available potassium and soil temperature (P<0.05), but not to soil water content. In some cases (corn straw with or without nitrogen fertilizer), straw residual rate was negatively correlated to straw water content, amino acid utilization and carboxylic acid utilization, and positively correlated with microbial species richness and evenness (P<0.05). Microbial community associated with corn and bean straw decomposition in soil was respectively dominated by aromatic- and polymer-metabolizing groups during the middle and late stages of this process, which could reduce the stability of microbial community structure and decrease the rate of straw decomposition in the fruit tree orchard.

submitted time 2021-02-10 From cooperative journals:《Journal of Arid Land》 Hits751Downloads409 Comment 0

2. chinaXiv:201705.00452 [pdf]

Lateral-Coupled Junctionless IZO-Based Electric-Double-Layer Thin-Film Transistors Gated by Solid-State Phosphosilicate Glass Electrolyte

Zhou, JM [Zhou Ju-Mei][ 1,2 ]; Gao, XH [Gao Xiao-Hong][ 1 ]; Zhang, HL [Zhang Hong-Liang][ 2 ]

We describe the lateral-coupled junctionless indium-zinc-oxide [IZO] thin-film transistors [TFTs] in which there are no junctions between channel and source/drain electrodes and with solid-state phosphosilicate glass electrolyte [PSG] gating. Due to the t

submitted time 2017-05-02 Hits720Downloads398 Comment 0

3. chinaXiv:201605.01803 [pdf]

PI3P phosphatase activity is required for autophagosome maturation and autolysosome formation

Wu, Yanwei; Wu, Yanwei; Cheng, Shiya; Zou, Wei; Wang, Xiaochen; Zhao, Hongyu; Zhang, Hong; Yoshina, Sawako; Mitani, Shohei; Yoshina, Sawako; Mitani, Shohei
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Autophagosome formation is promoted by the PI3 kinase complex and negatively regulated by myotubularin phosphatases, indicating that regulation of local phosphatidylinositol 3-phosphate (PtdIns3P) levels is important for this early phase of autophagy. Here, we show that the Caenorhabditis elegans myotubularin phosphatase MTM-3 catalyzes PtdIns3P turnover late in autophagy. MTM-3 acts downstream of the ATG-2/EPG-6 complex and upstream of EPG-5 to promote autophagosome maturation into autolysosomes. MTM-3 is recruited to autophagosomes by PtdIns3P, and loss of MTM-3 causes increased autophagic association of ATG-18 in a PtdIns3P-dependent manner. Our data reveal critical roles of PtdIns3P turnover in autophagosome maturation and/or autolysosome formation.

submitted time 2016-05-18 Hits11507Downloads1773 Comment 0

4. chinaXiv:201605.01733 [pdf]

Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy

Wu, Fan; Qi, Xin; Zhao, Hong-Yu; Wang, Zheng; Zhang, Hui; Ren, Jin-Qi; Feng, Wei; Hu, Jun-Jie; Zhang, Hong; Watanabe, Yasunori; Fujioka, Yuko; Noda, Nobuo N.; Guo, Xiang-Yang; Fang, Tian-Cheng; Wang, Peng; Shen, Yu-Xian
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Multicellular organisms have multiple homologs of the yeast ATG8 gene, but the differential roles of these homologs in autophagy during development remain largely unknown. Here we investigated structure/function relationships in the two C. elegans Atg8 homologs, LGG-1 and LGG-2. lgg-1 is essential for degradation of protein aggregates, while lgg-2 has cargo-specific and developmental-stage-specific roles in aggregate degradation. Crystallography revealed that the N-terminal tails of LGG-1 and LGG-2 adopt the closed and open form, respectively. LGG-1 and LGG-2 interact differentially with autophagy substrates and Atg proteins, many of which carry a LIR motif. LGG-1 and LGG-2 have structurally distinct substrate binding pockets that prefer different residues in the interacting LIR motif, thus influencing binding specificity. Lipidated LGG-1 and LGG-2 possess distinct membrane tethering and fusion activities, which may result from the N-terminal differences. Our study reveals the differential function of two ATG8 homologs in autophagy during C. elegans development.

submitted time 2016-05-15 Hits11044Downloads1645 Comment 0

5. chinaXiv:201605.01520 [pdf]

Effect of UBXD8 Deletion on Lipid Metabolism in Skeletal Muscle Cells

Zou Fei; Diao Zhi-Qing; Xu Shi-Meng; Liu Ping-Sheng; Liang Bie; Zhang Hong-Chao; Wei Xuan
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

UBXD8 is a membrane protein that mediates endoplasmic reticulum-associated protein ubiquitination and degradation by interacting with p97NCP. Recently, lipid droplet proteomic studies show the lipid droplet localization of UBXD8. Besides, UBXD8 is also involved in triglyceride metabolism. However, the molecular mechanism by which UBXD8 regulates triglyceride metabolism is still obscure. Here we knocked out UBXD8 in mouse C2C12 myoblasts by CRISPR/Cas9. We selected 2 UBXD8 knockout (KO) clone cell lines from 26 possible KO clones. UBXD8 KO did not change the lipid droplet proteins expression pattern. However, UBXD8 KO led to the accumulation of neutral lipid. Furthermore, our data show that UBXD8 KO could alleviate palmitate-induced insulin resistance and rescue palmitate-induced apoptosis which was characterized by PARP splicing. In addition, the phenotype of palmitate-induced insulin resistance and apoptosis was reappeared after overexpressing UBXD8 in UBXD8 KO cells. These data suggested that UBXD8 plays an important role in lipid metabolism and its abnormity related insulin signal and apoptosis.

submitted time 2016-05-12 Hits11155Downloads2171 Comment 0

6. chinaXiv:201605.01481 [pdf]

LSY-2 is essential for maintaining the germ-soma distinction in C-elegans

Lin, Long; Lin, Long; Yan, Libo; Zhao, Yu; Lin, Long; Li, Yuping; Zhang, Gangming; Zhang, Hong
Subjects: Biology >> Biophysics >> Cell Biology

The mechanisms that specify and maintain the characteristics of germ cells during animal development are poorly understood. In this study, we demonstrated that loss of function of the zinc-finger gene lsy-2 results in various somatic cells adopting germ cells characteristics, including expression of germline-specific P granules, enhanced RNAi activity and transgene silencing. The soma to germ transformation in lsy-2 mutants requires the activities of multiple chromatin remodeling complexes, including the MES-4 complex and the ISW-1 complex. The distinct germline-specific features in somatic cells and the gene expression profile indicate that LSY-2 acts in the Mec complex in this process. Our study demonstrated that lsy-2 functions in the maintenance of the soma-germ distinction.

submitted time 2016-05-12 Hits2610Downloads1490 Comment 0

7. chinaXiv:201605.01479 [pdf]

Identification of lipid droplet structure-like/resident proteins in Caenorhabditis elegans

Na, Huimin; Zhang, Peng; Chen, Yong; Zhu, Xiaotong; Liu, Yi; Liu, Yangli; Xie, Kang; Yang, Fuquan; Zhang, Hong; Liu, Pingsheng; Na, Huimin; Zhang, Peng; Zhu, Xiaotong; Liu, Yangli; Xie, Kang; Xu, Ningyi; Mak, Ho Yi; Xu, Ningyi; Mak, Ho Yi; Yu, Yong
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

The lipid droplet (LD) is a cellular organelle that stores neutral lipids in cells and has been linked with metabolic disorders. Caenorhabditis elegans has many characteristics which make it an excellent animal model for studying LDs. However, unlike in mammalian cells, no LD structure-like/resident proteins have been identified in C. elegans, which has limited the utility of this model for the study of lipid storage and metabolism. Herein based on three lines of evidence, we identified that MDT-28 and DHS-3 previously identified in C. elegans LD proteome were two LD structure-like/resident proteins. First, MDT-28 and DHS-3 were found to be the two most abundant LD proteins in the worm. Second, the proteins were specifically localized to LDs and we identified the domains responsible for this targeting in both proteins. Third and most importantly, the depletion of MDT-28 induced LD clustering while DHS-3 deletion reduced triacylglycerol content (TAG). We further characterized the proteins finding that MDT-28 was ubiquitously expressed in the intestine, muscle, hypodermis, and embryos, whereas DHS-3 was expressed mainly in intestinal cells. Together, these two LD structure-like/resident proteins provide a basis for future mechanistic studies into the dynamics and functions of LDs in C. elegans. (C) 2015 Elsevier B.V. All rights reserved.

submitted time 2016-05-12 Hits2163Downloads1082 Comment 0

8. chinaXiv:201605.01461 [pdf]

Guidelines for monitoring autophagy in Caenorhabditis elegans

Zhang, Hong; Guo, Bin; Lin, Long; Lu, Qun; Wu, Fan; Chang, Jessica T.; Hansen, Malene; Kumsta, Caroline; Lapierre, Louis R.; Jia, Kailiang; Kovacs, Attila L.; Legouis, Renaud; Melendez, Alicia; Melendez, Alicia; O'Rourke, Eyleen J.; Sato, Ken; Sato, Miyuki; Wang, Xiaochen
Subjects: Biology >> Biophysics >> Cell Biology

The cellular recycling process of autophagy has been extensively characterized with standard assays in yeast and mammalian cell lines. In multicellular organisms, numerous external and internal factors differentially affect autophagy activity in specific cell types throughout the stages of organismal ontogeny, adding complexity to the analysis of autophagy in these metazoans. Here we summarize currently available assays for monitoring the autophagic process in the nematode C. elegans. A combination of measuring levels of the lipidated Atg8 ortholog LGG-1, degradation of well-characterized autophagic substrates such as germline P granule components and the SQSTM1/p62 ortholog SQST-1, expression of autophagic genes and electron microscopy analysis of autophagic structures are presently the most informative, yet steady-state, approaches available to assess autophagy levels in C. elegans. We also review how altered autophagy activity affects a variety of biological processes in C. elegans such as L1 survival under starvation conditions, dauer formation, aging, and cell death, as well as neuronal cell specification. Taken together, C. elegans is emerging as a powerful model organism to monitor autophagy while evaluating important physiological roles for autophagy in key developmental events as well as during adulthood.

submitted time 2016-05-12 Hits2453Downloads1531 Comment 0

9. chinaXiv:201605.01388 [pdf]

Changes in Anti-Thyroglobulin IgG Glycosylation Patterns in Hashimoto's Thyroiditis Patients

Yuan, Shanshan; Zhang, Yang; Liu, Yalei; Yu, Nan; Zhang, Hong; Lu, Guizhi; Gao, Yanming; Gao, Ying; Guo, Xiaohui; Li, Qianqian; Huang, Chuncui; Wu, Hongmei; Li, Yan
Subjects: Biology >> Biophysics

Objective: Sera of Hashimoto's thyroiditis (HT) patients are known to exhibit elevated levels of anti-thyroglobulin IgG (TgAb IgG). Therefore, TgAb IgG represents a hallmark of this debilitating autoimmune disease. The aim of our study was to investigate the differential expression of specific glycosylation patterns of TgAb IgG from HT patients and healthy blood donors. Methods: HT patients (n = 32) were divided into two subgroups, medium level group (mHT, n = 15) and high level group (hHT, n = 17), according to the serum levels of TgAb detected by electrochemiluminescence immunoassay. TgAb IgG was purified by affinity chromatography from the sera of the HT group and control group (n = 15). MALDI-QIT-TOF-MS/MS spectrometry was performed to identify the glycosylation profiles of purified TgAb IgG. Lectin microarray technology was used to compare the abundance of different glycans found on TgAb IgG between HT patients and controls, and between the mHT and hHT groups. Results: The results by MALDI-QIT-TOF-MS/MS showed that the glycosylation profiles of TgAb IgG were similar between the mHT, hHT, and control groups. Furthermore, the lectin microarray showed that compared to the control group (all P < .001), there were higher levels present of (1) mannose (detected as lectin LCA, VFA, and MNA-M); (2) terminal sialic acid (detected as SNA-I and PSA); (3) core fucose (detected as LcH); and (4) Gal(beta 1-4) GlcNAc(beta 1-2) Man glycans (detected as PHA-L) on TgAb IgG from the HT group. A similar trend was observed between the hHT and mHT group, with elevated levels of mannose, terminal sialic acid, core fucose, and Gal(beta 1-4) GlcNAc(< 12) Man glycans on TgAb IgG found in the hHT group compared with the mHT group (all P < .05). Conclusions: TgAb IgG of HT patients exhibits higher glycosylation levels than those observed for TgAb IgG of healthy controls. Our results provide new clues for exploring the role of TgAb in the pathogenesis of HT.

submitted time 2016-05-12 Hits1614Downloads935 Comment 0

10. chinaXiv:201605.01370 [pdf]

MutM Interaction Partners Detected in Mycobacterium smegmatis by Tandem Affinity Purification

Fan Shang-Hua; Yu Zi-Niu; Fan Shang-Hua; Zhou Ying; Zhang Hong-Tai; Fleming, Joy; Zhang Xian-En; Bi Li-Jun; Fan Shang-Hua; Zhou Ying; Zhang Hong-Tai; Fleming, Joy; Zhang Xian-En; Bi Li-Jun
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

MutM (Formamidopyrimidine-DNA glycosylase, Fpg), a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase), is involved in the repair of many kinds of DNA damage, including the formation of 8-oxoguanine, 5-formyluracil, and C/C mismatches, through recognizing DNA damage and removing damaged bases. The mechanisms of MutM involvement, however, with the exception of 8-oxoG, are poorly understood. Here, we identified proteins which interact with MutM in Mycobacterium smegmatis using methods of tandem affinity purification and mass spectrometry and used Far-western and GST pull-down analysis to validate the interactions between MutM and DEAD-box rna helicase, RpsC, and UvrA. Results demonstrated that tandem affinity purification is a suitable method for identifying MutM interacting proteins and provided insights into the mechanism by which MutM is involved in DNA damage repair.

submitted time 2016-05-12 Hits7289Downloads1360 Comment 0

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