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1. chinaXiv:202111.00045 [pdf]

Succession of soil bacterial and fungal communities of Caragana korshinskii plantation in a typical agro-pastoral ecotone in northern China over a 50-a period

MA Gailing; GOU Qianqian; WANG Guohua; QU Jianjun
Subjects: Geosciences >> Geography

Bacterial and fungal communities play critical roles in reestablishing vegetation structure, function and biodiversity in ecosystem restoration in arid and semi-arid areas. However, the long-term successional changes in bacterial and fungal communities that occur with artificial vegetation development are not fully understood. In this study, we investigated the successional changes in bacterial and fungal communities in Caragana korshinskii Kom. plantation over a period of 50 a (6, 12, 18, 40 and 50 a) and their relationships with key soil environmental factors in a typical agro-pastoral ecotone, northern China. The results showed that bacterial and fungal diversities (α- and β-diversity) were significantly affected by plantation age; moreover, the change in fungal community was more evident than that in bacterial community. Soil samples from 12 a plantation had the highest (P<0.05) bacterial and fungal α-diversity (i.e., abundance-based coverage estimator (ACE) and Chao1 index) at 0–10 cm depth compared with other samples. However, soil samples from plantation at the late recovery stage (40–50 a) had the highest α-diversity at 10–20 cm depth. Soil bacterial community was not significantly affected by plantation age at the genus level; but, soil fungal community was significantly affected at the genus level. Overall, Mortierella and Chaetomium were the dominant genera at natural recovery stage (0 a); Inocybe was the dominant genus at the early recovery stage (6–12 a); Inocybe and Mortierella were the dominant genera at the mid-recovery stage (12–40 a); And Mortierella, Cladosporium and Humicola were the dominant genera at the late recovery stage (40–50 a). Redundancy analysis (RDA) showed that β-glucosidase activity, total nitrogen and soil organic carbon were closely associated with bacterial community composition, while alkaline phosphatase, urease activity and total nitrogen were associated with fungal community composition, indicating that changes in enzyme activity and soil nutrients were the most important determinants of dominant genera. Furthermore, pathogenic microorganisms (Cladosporium and Humicola) were dominant in soils from 40–50 a plantation, which may affect plant growth, resulting in the decline of C. korshinskii plantation. Overall, the findings of this study improve the understanding of ecological patterns of bacterial and fungal communities in artificial vegetation and provide an important scientific basis for comprehensive ecological restoration management in arid and semi-arid areas.

submitted time 2021-11-10 Cooperative journals:《Journal of Arid Land》 Hits2011Downloads292 Comment 0

2. chinaXiv:202104.00020 [pdf]

Bacterial and viral therapies of cancer background, mechanism and perspective

Qinglin Dong, Xiangying Xing
Subjects: Medicine, Pharmacy >> Preclinical Medicine

Bacterial and viral therapies of cancer are highly promising, yet their mechanisms are incompletely understood, hindering their improvement and application. In this paper, We (1) review briefly the genesis and progress of bacterial and viral therapies of cancer, (2) compare and evaluate the proposed mechanisms of bacterial and viral therapies of cancer and present the unifying mechanism that bacteria/viruses stimulate cancer cells to produce antibacterial/antiviral proteins, which also serve as the responsive cancer antigens triggering host anticancer immune response, and (3) provide a perspective on the exploitation of non-human and non-animal bacteria and viruses, particularly protist-infecting bacteria and viruses and bacterial virus (bacteriophage/phage), for cancer treatment and prevention.

submitted time 2021-04-29 Hits20061Downloads1223 Comment 0

3. chinaXiv:202011.00137 [pdf]

Endophytic bacteria associated with halophyte Seidlitzia rosmarinus Ehrenb. ex Boiss. from saline soil of Uzbekistan and their plant beneficial traits

SHURIGIN,Vyacheslav ; EGAMBERDIEVA,Dilfuza ; LI,Li; DAVRANOV,Kakhramon ; PANOSYAN,Hovik ; BIRKELAND,Nils-K?re ; WIRTH,Stephan ; BELLINGRATH-KIMURA,Sonoko D
Subjects: Geosciences >> Marine Sciences

Endophytic bacteria of halophytic plants play essential roles in salt stress tolerance. Therefore, an understanding of the true nature of plant–microbe interactions under extreme conditions is essential. The current study aimed to identify cultivable endophytic bacteria associated with the roots and shoots of Seidlitzia rosmarinus Ehrenb. ex Boiss. grown in the salt-affected soil in Uzbekistan and to evaluate their plant beneficial traits related to plant growth stimulation and stress tolerance. Bacteria were isolated from the roots and the shoots of S. rosmarinus using culture-dependent techniques and identified by the 16S rRNA gene. RFLP (Restriction Fragment Length Polymorphism) analysis was conducted to eliminate similar isolates. Results showed that the isolates from the roots of S. rosmarinus belonged to the genera Rothia, Kocuria, Pseudomonas, Staphylococcus, Paenibacillus and Brevibacterium. The bacterial isolates from the shoots of S. rosmarinus belonged to the genera Staphylococcus, Rothia, Stenotrophomonas, Brevibacterium, Halomonas, Planococcus, Planomicrobium and Pseudomonas, which differed from those of the roots. Notably, Staphylococcus, Rothia and Brevibacterium were detected in both roots and shoots, indicating possible migration of some species from roots to shoots. The root-associated bacteria showed higher levels of IAA (indole-3-acetic acid) synthesis compared with those isolated from the shoots, as well as the higher production of ACC (1-aminocyclopropane-1-carboxylate) deaminase. Our findings suggest that halophytic plants are valuable sources for the selection of microbes with a potential to improve plant fitness under saline soils.

submitted time 2020-11-25 Cooperative journals:《Journal of Arid Land》 Hits2613Downloads833 Comment 0

4. chinaXiv:201811.00103 [pdf]

Changes in soil microbial community response to precipitation events in a semi-arid steppe of the Xilin River Basin, China

ZHANG Hui; LIU Wenjun; KANG Xiaoming; CUI Xiaoyong; WANG Yanfen; ZHAO Haitao; QIAN Xiaoqing; HAO Yanbin
Subjects: Agriculture, Forestry,Livestock & Aquatic Products Science >> Soil Science

In the context of climate change, precipitation is predicted to become more intense at the global scale. Such change may alter soil microbial communities and the microbially mediated carbon and nitrogen dynamics. In this study, we experimentally repackaged precipitation patterns during the growing season (from June to September) of 2012 in a semi-arid temperate steppe of the Xilin River Basin in Inner Mongolia of China, based on the 60-year growing season precipitation data. Specifically, we manipulated a total amount of 240 mm precipitation to experimental plots by taking the following treatments: (1) P6 (6 extreme precipitation events, near the 1st percentile); (2) P10 (10 extreme precipitation events, near the 5th percentile); (3) P16 (16 moderate precipitation events, near the 50th percentile); and (4) P24 (24 events, 60-year average precipitation, near the 50th percentile). At the end of the growing season, we analyzed soil microbial community structure and biomass, bacterial abundance, fungal abundance and bacterial composition, by using phospholipid fatty acid (PLFA), real-time quantitative polymerase chain reaction (RT-qPCR) and 16S rRNA gene clone library methods. The extreme precipitation events did not change soil microbial community structure (represented by the ratio of PLFA concentration in fungi to PLFA concentration in bacteria, and the ratio of PLFA concentration in gram-positive bacterial biomass to PLFA concentration in gram-negative bacterial biomass). However, the extreme precipitation events significantly increased soil microbial activity (represented by soil microbial biomass nitrogen and soil bacterial 16S rRNA gene copy numbers). Soil fungal community showed no significant response to precipitation events. According to the redundancy analysis, both soil microbial biomass nitrogen and soil ammonium nitrogen (NH4-N) were found to be significant in shaping soil microbial community. Acidobacteria, Actinobacteria and Proteobacteria were the dominant phyla in soil bacterial composition, and responded differently to the extreme precipitation events. Based on the results, we concluded that the extreme precipitation events altered the overall soil microbial activity, but did not impact how the processes would occur, since soil microbial community structure remained unchanged.

submitted time 2018-11-23 Cooperative journals:《Journal of Arid Land》 Hits14074Downloads2043 Comment 0

5. chinaXiv:201605.01806 [pdf]

Polymer-Ag Nanocomposites with Enhanced Antimicrobial Activity against Bacterial Infection

Mei, Lin; Lu, Zhentan; Zhang, Xinge; Li, Chaoxing; Jia, Yanxia; Jia, Yanxia
Subjects: Biology >> Biophysics

Herein, a nontoxic nanocomposite is synthesized by reduction of silver nitrate in the presence of a cationic polymer displaying strong antimicrobial activity against bacterial infection. These nanocomposites with a large concentration of positive charge promote their adsorption to bacterial membranes through electrostatic interaction. Moreover, the synthesized nanocomposites with polyvalent and synergistic antimicrobial effects can effectively kill both Gram-positive and Gram-negative bacteria without the emergence of bacterial resistance. Morphological changes obtained by transmission electron microscope observation show that these nanocomposites can cause leakage and chaos of intracellular contents. Analysis of the antimicrobial mechanism confirms that the lethal action of nanocomposites against the bacteria started with disruption of the bacterial membrane, subsequent cellular internalization of the nanopartides, and inhibition of intracellular enzymatic activity. This novel antimicrobial material with good cytocompatibility promotes healing of infected wounds in diabetic rats, and has a promising future in the treatment of other infectious diseases.

submitted time 2016-05-18 Hits4162Downloads2031 Comment 0

6. 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 Hits11628Downloads2495 Comment 0

7. chinaXiv:201605.01344 [pdf]

Discovery and characterization of Ku acetylation in Mycobacterium smegmatis

Zhou, Ying; Fleming, Joy; Wang, Liwei; Wang, Yingying; Zhang, Xiaoli; Wei, Wenjing; Bi, Lijun; Chen, Tao; Zhou, Lin; Deng, Jiaoyu; Wang, Xude
Subjects: Biology >> Biophysics

Lysine acetylation is an important post-translational modification and is known to regulate many eukaryotic cellular processes. Little, however, is known about acetylated proteins in prokaryotes. Here, using immunoblotting, mass spectrometry and mutagenesis studies, we investigate the acetylation dynamics of the DNA repair protein Ku and its relationship with the deacetylase protein Sir2 and the non-homologous end joining (NHEJ) pathway in Mycobacterium smegmatis. We report that acetylation of Ku increases with growth, while NHEJ activity decreases, providing support for the hypothesis that acetylation of Ku may be involved in the DNA damage response in bacteria. Ku has multiple lysine sites. Our results indicate that K29 is an important acetylation site and that deficiency of Sir2 or mutation of K29 affects the quantity of Ku and its acetylation dynamics. Our findings expand knowledge of acetylation targets in prokaryotes and indicate a new direction for further research on bacterial DNA repair mechanisms.

submitted time 2016-05-11 Hits1971Downloads1172 Comment 0

8. chinaXiv:201605.01336 [pdf]

Non-canonical activation of inflammatory caspases by cytosolic LPS in innate immunity

Yang, Jieling; Shao, Feng; Yang, Jieling; Zhao, Yue; Shao, Feng
Subjects: Biology >> Biophysics >> Immunology

Lipopolysaccharide (LPS) is the major component of Gram-negative bacteria cell wall. In innate immunity, extracellular LPS is recognized by Toll-like receptor 4 to stimulate cytokine transcription. Recent studies suggest a 'non-canonical inflammasome' that senses cytoplasmic LPS and activates caspase-11 in mouse macrophages. Unexpectedly, biochemical studies reveal that caspase-11 and its human orthologs caspase-4/caspase-5 are LPS receptors themselves. Direct LPS binding induces caspase-4/caspase-5/caspase-11 oligomerization and activation, triggering cell pyroptosis and anti-bacterial defenses. Caspase-4/caspase-5/caspase-11 recognition of intracellular LPS requires bacterial escape from the vacuole; this process is promoted by interferon-inducible GTPases-mediated lysis of the bacteria-containing vacuole. Non-canonical activation of these inflammatory caspases by LPS not only represents a new paradigm in innate immunity but also critically determines LPS-induced septic shock in mice.

submitted time 2016-05-11 Hits2922Downloads1509 Comment 0

9. chinaXiv:201605.01296 [pdf]

Plasmacytoid dendritic cells promote HIV-1-induced group 3 innate lymphoid cell depletion

Zhang, Zheng; Zhao, Juanjuan; Wang, Fu-Sheng; Zhang, Zheng; Cheng, Liang; Li, Guangming; Reszka-Blanco, Natalia J.; Sum, Lishan; Zhang, Zheng; Zhao, Juanjuan; Zhang, Liguo; Sum, Lishan; Chen, Weiwei; Nie, Weiming; Wang, Fu-Sheng
Subjects: Biology >> Biophysics

Group 3 innate lymphoid cells (ILC3s) have demonstrated roles in promoting antibacterial immunity, maintaining epithelial barrier function, and supporting tissue repair. ILC3 alterations are associated with chronic inflammation and inflammatory disease; however, the characteristics and relevant regulatory mechanisms of this cell population in HIV-1 infection are poorly understood due in part to a lack of a robust model. Here, we determined that functional human ILC3s develop in lymphoid organs of humanized mice and that persistent HIV-1 infection in this model depletes ILC3s, as observed in chronic HIV-1-infected patients. In HIV-1-infected mice, effective antiretroviral therapy reversed the loss of ILC3s. HIV-1-dependent reduction of ILC3s required plasmacytoid dendritic cells (pDCs), IFN-I, and the CD95/FasL pathway, as targeted depletion or blockade of these prevented HIV-1-induced ILC3 depletion in vivo and in vitro, respectively. Finally, we determined that HIV-1 infection induces CD95 expression on ILC3s via a pDC- and IFN-I-dependent mechanism that sensitizes ILC3s to undergo CD95/FasL-mediated apoptosis. We conclude that chronic HIV-1 infection depletes ILC3s through pDC activation, induction of IFN-I, and CD95-mediated apoptosis.

submitted time 2016-05-11 Hits1956Downloads1174 Comment 0

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