Phenanthrene binding by humic acid–protein complexes as studied by passive dosing technique

2014 ◽  
Vol 184 ◽  
pp. 145-153 ◽  
Author(s):  
Jian Zhao ◽  
Zhenyu Wang ◽  
Saikat Ghosh ◽  
Baoshan Xing
Biochimie ◽  
2017 ◽  
Vol 137 ◽  
pp. 139-146 ◽  
Author(s):  
Mehboob Hoque ◽  
Jyoti Gupta ◽  
M. Saleemuddin

Molecules ◽  
2019 ◽  
Vol 24 (1) ◽  
pp. 179 ◽  
Author(s):  
Dariusz Mrozek ◽  
Tomasz Dąbek ◽  
Bożena Małysiak-Mrozek

Calculation of structural features of proteins, nucleic acids, and nucleic acid-protein complexes on the basis of their geometries and studying various interactions within these macromolecules, for which high-resolution structures are stored in Protein Data Bank (PDB), require parsing and extraction of suitable data stored in text files. To perform these operations on large scale in the face of the growing amount of macromolecular data in public repositories, we propose to perform them in the distributed environment of Azure Data Lake and scale the calculations on the Cloud. In this paper, we present dedicated data extractors for PDB files that can be used in various types of calculations performed over protein and nucleic acids structures in the Azure Data Lake. Results of our tests show that the Cloud storage space occupied by the macromolecular data can be successfully reduced by using compression of PDB files without significant loss of data processing efficiency. Moreover, our experiments show that the performed calculations can be significantly accelerated when using large sequential files for storing macromolecular data and by parallelizing the calculations and data extractions that precede them. Finally, the paper shows how all the calculations can be performed in a declarative way in U-SQL scripts for Data Lake Analytics.


2008 ◽  
Vol 72 (8) ◽  
pp. 2090-2099 ◽  
Author(s):  
W.F. Tan ◽  
L.K. Koopal ◽  
L.P. Weng ◽  
W.H. van Riemsdijk ◽  
W. Norde

2019 ◽  
Author(s):  
Ece Kocak ◽  
Sarah Dykstra ◽  
Alexandra Nemeth ◽  
Catherine G. Coughlin ◽  
Kasey Rodgers ◽  
...  

AbstractPIF1 is a 5’ to 3’ DNA helicase that can unwind double-stranded DNA and disrupt nucleic acid-protein complexes. In Saccharomyces cerevisiae, Pif1 plays important roles in mitochondrial and nuclear genome maintenance, telomere length regulation, unwinding of G-quadruplex structures, and DNA synthesis during break-induced replication. Some, but not all, of these functions are shared with other eukaryotes. To gain insight into the evolutionarily conserved functions of PIF1, we created pif1 null mutants in Drosophila melanogaster and assessed their phenotypes throughout development. We found that pif1 mutant larvae exposed to high concentrations of hydroxyurea, but not other DNA damaging agents, experience reduced survival to adulthood. Embryos lacking PIF1 fail to segregate their chromosomes efficiently during early nuclear divisions, consistent with a defect in DNA replication. Furthermore, loss of the BRCA2 protein, which is required for stabilization of stalled replication forks in metazoans, causes synthetic lethality in third instar larvae lacking either PIF1 or the polymerase delta subunit POL32. Interestingly, pif1 mutants have a reduced ability to synthesize DNA during repair of a double-stranded gap, but only in the absence of POL32. Together, these results support a model in which Drosophila PIF1 functions with POL32 during times of replication stress but acts independently of POL32 to promote synthesis during double-strand gap repair.


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