residue type
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2022 ◽  
Vol 172 ◽  
pp. 104349
Author(s):  
Resham Thapa ◽  
Katherine L. Tully ◽  
Nora Hamovit ◽  
Stephanie A. Yarwood ◽  
Harry H. Schomberg ◽  
...  

2022 ◽  
Vol 14 (2) ◽  
pp. 864
Author(s):  
Opinder Singh Sandhu ◽  
Mangi L. Jat ◽  
Rajeev Kumar Gupta ◽  
Harmeet Singh Thind ◽  
Harminder Singh Sidhu ◽  
...  

Decomposition influences carbon and nutrient cycling from crop residues. The nylon-mesh-bag technique was implied to study the decomposition and N-release dynamics from different crop residues under field conditions. The four types of residues were: maize (lower than 50% below the cob), wheat (lower than 25% of wheat stubbles), a whole mung bean residue, and a mixture of wheat + mung bean residue (1:1 ratio) put on the soil surface and in below the sub-surface. Decomposition and N release from both at-surface- and below-surface-placed residues were accurately described by a single-pool first-order exponential decay function as a function of thermal time (based on the accumulative daily mean temperature). The simple first-order exponential model met the criteria of goodness of fit. Throughout the decomposition cycle (one thermal year), the rate of decomposition as measured by a decrease in residue mass and the release of total N were statistically higher from the sub-surface compared to the surface-placed residue, irrespective of the residue type. At the end of the 150-day decomposition cycle, the release of total N was highest in mung bean (32.0 kg N ha−1), followed by maize (31.5 kg N ha−1) > wheat + mung bean (16.1 kg N ha−1), and the minimum (6.54 kg N ha−1) in wheat residue. Crop residues with a wider C/N ratio such as maize and wheat, when applied on the soil surface in conservation agriculture, caused the decomposition to occur at slower rates, thereby providing long-term beneficial effects on the soil thermal regime, soil moisture conservation, and C sequestration in North-West India.


2021 ◽  
Author(s):  
Haim J. Wolfson ◽  
Mark Rozanov

The cryo-EM resolution revolution enables the development of algorithms for direct de-novo modelling of protein structures from given cryo-EM density maps. Deep Learning tools have been applied to locate structure patterns, such as rotamers, secondary structures and Cα atoms. We present a deep neural network (nicknamed SegmA) for the residue type segmentation of a cryo-EM density map. The network labels voxels in a cryo-EM map by the residue type (amino acid type or nucleic acid) of the sampled macromolecular structure. It also provides a visual representation of the density map by coloring the different types of voxels by their assgned colors. SegmA's algorithm combines a rotation equivariant group convolutional network with a traditional U-net network in a cascade. In addition SegmA estimates the labeling accuracy and reports only labels assigned with high confidence. At resolution of 3 Å SegmAs accuracy is 80% for nucleotides. Amino acids which can be seen by eye, such as LEU, ARG and PHE, are detected by Segma with about 70% accuracy. A web server of the application is under development at https://dev.dcsh7cbr3o89e.amplifyapp.com. The SegmA open code is available at https://github.com/Mark-Rozanov/SegmA_3A/ tree/master .


2021 ◽  
Author(s):  
Ninghui Xie ◽  
Sean Michael Schaeffer ◽  
Tingting An ◽  
Yingde Xu ◽  
Shuangyi Li ◽  
...  

Abstract The labile organic carbon (C) pool plays a vital role in soil biogeochemical transformation and can be used as a sensitive indicator of the response of soil quality to agricultural practice. However, little is known about how residue type and soil fertilization affect the incorporation of residue C into labile organic C pools. A 360-day laboratory incubation was conducted with the addition of 13C-labeled maize residues (root, stem and leaf) to unfertilized and organic-fertilized soils. A greater contribution of residue C to extractable organic C (EOC, 7.2%) was observed in the unfertilized soil than that in the organic-fertilized soil (6.0%). The contribution of residue C to microbial biomass C (MBC) was 20%-50% in the organic-fertilized soil, but only 10%-30% in the unfertilized soil. This suggests that, in organic-fertilized soil, there is accelerated transformation of residue C into microbial biomass and a higher capacity for residue C stabilization through greater, or more efficient anabolism. Moreover, the distribution of leaf C into MBC was higher than that from root and stem in the unfertilized soil, whereas more root C entered to EOC and MBC than from stem and leaf in the organic-fertilized soil. This shows that maize root can also be involved in microbial assimilation, but it depends on the initial soil nutrition. Overall, these findings deepen our understanding of the mechanisms of microbe-mediated C transformation processes, and provide relevant insights into the capture and incorporation of plant residue C into labile organic C pools driven by residue type and soil fertilization.


CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7380-7388
Author(s):  
Eline Grothe ◽  
Hugo Meekes ◽  
René de Gelder
Keyword(s):  

Multicomponent crystals in the CSD are classified into 49 subclasses based on chirality and residue type.


Entropy ◽  
2019 ◽  
Vol 21 (8) ◽  
pp. 764 ◽  
Author(s):  
Eshel Faraggi ◽  
A. Keith Dunker ◽  
Robert L. Jernigan ◽  
Andrzej Kloczkowski

Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and disorder information. We introduced several parameters as measures of fluctuations at a given MSA site and used these as representative of the sequence and structure entropy at that site. In general, we found a tendency for negative correlations between disorder and structure, and significant positive correlations between disorder and the fluctuations in the system. We also found evidence for residue-type conservation for those residues proximate to potentially disordered sites. Mutation at the disorder site itself appear to be allowed. In addition, we found positive correlation for disorder and accessible surface area, validating that disordered residues occur in exposed regions of proteins. Finally, we also found that fluctuations in the dihedral angles at the original mutated residue and disorder are positively correlated while dihedral angle fluctuations in spatially proximal residues are negatively correlated with disorder. Our results seem to indicate permissible variability in the disordered site, but greater rigidity in the parts of the protein with which the disordered site interacts. This is another indication that disordered residues are involved in protein function.


2019 ◽  
Vol 10 (1) ◽  
pp. 37-50 ◽  
Author(s):  
Ashim Datta ◽  
H. S. Jat ◽  
A. K. Yadav ◽  
Madhu Choudhary ◽  
P. C. Sharma ◽  
...  

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