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1. 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 Hits2782Downloads1738 Comment 0

2. chinaXiv:201605.01180 [pdf]

Structural and Functional Characterization of Acinetobacter baumannii Nucleoside Diphosphate Kinase

Hu Ying-Song; Feng Feng; Liu Ying-Fang; Hu Ying-Song
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

A cinetobacter baumannii is a new threat in intensive care units (ICUs) for its multiresistance to antibiotics, but little is known about this bacterium. Nucleoside diphosphate kinase (NDK) is an evolutionarily conserved enzyme that catalyzes phosphoryl transformation between nucleosides. In our study, the crystal structure of wild type A cinetobacter baumannii NDK along with its mutant generated through truncation of the C-terminal arginine-threonine-arginine (RTR) residues, were solved. In comparison with Myxococcus xanthus NDK structure, we speculated that A cinetobacter baumannii NDK shared a similar catalytic mechanism with Myxococcus xanthus. Activity assay and CD spectra analysis revealed that E28A mutant might interrupt the secondary structure of the protein leading to declined enzymatic activity. Truncation of the C-terminal RTR residues would lead to the instability of the tertiary structure resulting in reduced kinase activity. Lys33 was a key residue for maintaining dimer interaction when RTR residues were truncated but was not sufficient to keep efficient enzymatic reaction. The structural data can provide a potential target to develop novel therapeutic approaches to overcome multiresistance of the bacterium against antibiotics.

submitted time 2016-05-11 Hits1100Downloads546 Comment 0

3. chinaXiv:201605.00480 [pdf]

Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics

Yashwant Kumar; Limin Zhang; Priyabrata Panigrahi; Bhushan B. Dholakia; Veena Dewangan; Sachin G. Chavan; Shrikant M. Kunjir; Xiangyu Wu; Ning Li; Pattuparambil R. Rajmohanan; Narendra Y. Kadoo; Ashok P. Giri; Huiru Tang; Vidya S. Gupta
Subjects: Biology >> Botany >> Plant biochemistry, plant Biophysics

Molecular changes elicited by plants in response to fungal attack and how this affects plant–pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label-free proteomics and NMR-based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis-related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea–Foc interactions.

submitted time 2016-05-04 Hits2677Downloads1630 Comment 0

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