scholarly journals β-elimination of hyaluronate by red king crab hyaluronidase

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dmitrii Sliadovskii ◽  
Tatyana Ponomareva ◽  
Maxim Molchanov ◽  
Irina Pozdnyakova-Filatova ◽  
Maria Timchenko ◽  
...  

AbstractCrustacean hyaluronidases are poorly understood both in terms of their enzymatic properties and in terms of their structural features. In this work, we show that the hepatopancreas homogenate of the red king crab has a hyaluronidase activity that is an order of magnitude higher than its commercial counterpart. Zymography revealed that the molecular weight of a protein with hyalorunidase activity is 40–50 kDa. Analysis of the hepatopancreas transcriptome and results of cloning and sequencing of cDNA revealed a hyaluronidase sequence with an expected molecular weight of 42.5 kDa. Further analysis showed that hyaluronat enzymatic cleavage follows the $$\beta $$ β -elimination mechanism, which is well known for bacterial hyaluronidases. The results of ion-exchange chromatography showed that the final product of hyaluronate degradation is unsaturated tetrasaccharide. Thus, we identified a new hyaluronidase of higher eukaryotes, which is not integrated into the modern classification of hyaluronidases.

Author(s):  
Dmitrii Sliadovskii ◽  
Tatyana Ponomareva ◽  
Maxim Molchanov ◽  
Irina Pozdnyakova-Filatova ◽  
Maria Timchenko ◽  
...  

Crustacean hyaluronidases are 1 poorly understood both in terms of their enzymatic properties and in terms of their structural features. In this work, we have shown that the hepatopancreas homogenate of the red king crab has a hyaluronidase activity that is an order of magnitude higher than its commercial counterpart. Zymography revealed the hyaluronidase activity of the protein roughly from40 to 50 kDa relative to the molecular marker used in electrophoresis. Analysis of the hepatopancreas transcriptome revealed a hyaluronidase sequence with an expected molecular weight of 42.5 kDa. It turned out that the reaction of cleavage of hyaluronate in the presence of a homogenate proceeds by the mechanism of b-elimination, which is well known for bacterial hyaluronidases. Thus, a new hyaluronidase of higher eukaryotes was found and described, which is not integrated into the modern classification of hyaluronidases.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abdulkadir Tasdelen ◽  
Baha Sen

AbstractmiRNAs (or microRNAs) are small, endogenous, and noncoding RNAs construct of about 22 nucleotides. Cumulative evidence from biological experiments shows that miRNAs play a fundamental and important role in various biological processes. Therefore, the classification of miRNA is a critical problem in computational biology. Due to the short length of mature miRNAs, many researchers are working on precursor miRNAs (pre-miRNAs) with longer sequences and more structural features. Pre-miRNAs can be divided into two groups as mirtrons and canonical miRNAs in terms of biogenesis differences. Compared to mirtrons, canonical miRNAs are more conserved and easier to be identified. Many existing pre-miRNA classification methods rely on manual feature extraction. Moreover, these methods focus on either sequential structure or spatial structure of pre-miRNAs. To overcome the limitations of previous models, we propose a nucleotide-level hybrid deep learning method based on a CNN and LSTM network together. The prediction resulted in 0.943 (%95 CI ± 0.014) accuracy, 0.935 (%95 CI ± 0.016) sensitivity, 0.948 (%95 CI ± 0.029) specificity, 0.925 (%95 CI ± 0.016) F1 Score and 0.880 (%95 CI ± 0.028) Matthews Correlation Coefficient. When compared to the closest results, our proposed method revealed the best results for Acc., F1 Score, MCC. These were 2.51%, 1.00%, and 2.43% higher than the closest ones, respectively. The mean of sensitivity ranked first like Linear Discriminant Analysis. The results indicate that the hybrid CNN and LSTM networks can be employed to achieve better performance for pre-miRNA classification. In future work, we study on investigation of new classification models that deliver better performance in terms of all the evaluation criteria.


2021 ◽  
Vol 240 ◽  
pp. 105964
Author(s):  
Cory Lescher ◽  
Noëlle Yochum ◽  
Brad Harris ◽  
Nathan Wolf ◽  
John Gauvin

2011 ◽  
Vol 68 (3) ◽  
pp. 499-506 ◽  
Author(s):  
W. Stewart Grant ◽  
Susan E. Merkouris ◽  
Gordon H. Kruse ◽  
Lisa W. Seeb

AbstractGrant, W. S., Merkouris, S. E., Kruse, G. H., and Seeb, L. W. 2011. Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure? – ICES Journal of Marine Science, 68: . Populations of red king crab in the North Pacific and Bering Sea have declined in response to ocean-climate shifts and to harvesting. An understanding of how populations are geographically structured is important to the management of these depressed resources. Here, the Mendelian variability at 38 enzyme-encoding loci was surveyed in 27 samples (n = 2427) from 18 general locations. Sample heterozygosities were low, averaging HE = 0.015 among samples. Weak genetic structure was detected among three groups of populations, the Bering Sea, central Gulf of Alaska, and Southeast Alaska, but without significant isolation by distance among populations. A sample from Adak Island in the western Aleutians was genetically different from the remaining samples. The lack of differentiation among populations within regions may, in part, be due to post-glacial expansions and a lack of migration-drift equilibrium and to limited statistical power imposed by low levels of polymorphism. Departures from neutrality may reflect the effects of both selective and historical factors. The low allozyme diversity in red king crab may, in part, be attributable to adaptive specialization, background selection, ice-age population bottlenecks, or metapopulation dynamics in a climatically unstable North Pacific.


2013 ◽  
Vol 71 (2) ◽  
pp. 365-373 ◽  
Author(s):  
Ann Merete Hjelset

Abstract Hjelset, A. M. 2014. Fishery-induced changes in Norwegian red king crab (Paralithodes camtschaticus) reproductive potential. – ICES Journal of Marine Science, 71: 365–373. The introduced red king crab (Paralithodes camtschaticus) in the Barents Sea supports a valuable fishery in northern Norway. In this paper, I examine the effect of the increased harvest rate and the recently added female quota on the potential egg production of the stock. The size ranges of males and females in the period 1995–2011 were recorded, and estimated stock abundance of ovigerous females and established individual fecundity parameters from 2000–2007 were used to assess the reproductive potential of the stock from 1995–2011. The upper size ranges of males and females decreased throughout the period studied, presumably mainly due to fishing. The change in size composition among ovigerous females and functional mature males, and the reduced mean individual fecundity in the stock seem to have had a negative effect on the potential egg production of the stock.


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