scholarly journals Discovery of Hyperactive Antifreeze Protein from Phylogenetically Distant Beetles Questions Its Evolutionary Origin

2021 ◽  
Vol 22 (7) ◽  
pp. 3637
Author(s):  
Tatsuya Arai ◽  
Akari Yamauchi ◽  
Ai Miura ◽  
Hidemasa Kondo ◽  
Yoshiyuki Nishimiya ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Freezing Point ◽  
Consensus Sequence ◽  
Antifreeze Protein ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Entire Surface ◽  
Chilled Storage ◽  
Peptide Region

Beetle hyperactive antifreeze protein (AFP) has a unique ability to maintain a supercooling state of its body fluids, however, less is known about its origination. Here, we found that a popular stag beetle Dorcus hopei binodulosus (Dhb) synthesizes at least 6 isoforms of hyperactive AFP (DhbAFP). Cold-acclimated Dhb larvae tolerated −5 °C chilled storage for 24 h and fully recovered after warming, suggesting that DhbAFP facilitates overwintering of this beetle. A DhbAFP isoform (~10 kDa) appeared to consist of 6−8 tandem repeats of a 12-residue consensus sequence (TCTxSxNCxxAx), which exhibited 3 °C of high freezing point depression and the ability of binding to an entire surface of a single ice crystal. Significantly, these properties as well as DNA sequences including the untranslated region, signal peptide region, and an AFP-encoding region of Dhb are highly similar to those identified for a known hyperactive AFP (TmAFP) from the beetle Tenebrio molitor (Tm). Progenitor of Dhb and Tm was branched off approximately 300 million years ago, so no known evolution mechanism hardly explains the retainment of the DNA sequence for such a lo­ng divergence period. Existence of unrevealed gene transfer mechanism will be hypothesized between these two phylogenetically distant beetles to acquire this type of hyperactive AFP.

scholarly journals Growth suppression of ice crystal basal face in the presence of a moderate ice-binding protein does not confer hyperactivity

2018 ◽  
Vol 115 (29) ◽  
pp. 7479-7484 ◽  
Author(s):  
Maddalena Bayer-Giraldi ◽  
Gen Sazaki ◽  
Ken Nagashima ◽  
Sepp Kipfstuhl ◽  
Dmitry A. Vorontsov ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Heat Dissipation ◽  
Freezing Point ◽  
Binding Protein ◽  
Ice Crystals ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Basal Face ◽  
Ice Binding ◽  
Ice Binding Protein

Ice-binding proteins (IBPs) affect ice crystal growth by attaching to crystal faces. We present the effects on the growth of an ice single crystal caused by an ice-binding protein from the sea ice microalga Fragilariopsis cylindrus (fcIBP) that is characterized by the widespread domain of unknown function 3494 (DUF3494) and known to cause a moderate freezing point depression (below 1 °C). By the application of interferometry, bright-field microscopy, and fluorescence microscopy, we observed that the fcIBP attaches to the basal faces of ice crystals, thereby inhibiting their growth in the c direction and resulting in an increase in the effective supercooling with increasing fcIBP concentration. In addition, we observed that the fcIBP attaches to prism faces and inhibits their growth. In the event that the effective supercooling is small and crystals are faceted, this process causes an emergence of prism faces and suppresses crystal growth in the a direction. When the effective supercooling is large and ice crystals have developed into a dendritic shape, the suppression of prism face growth results in thinner dendrite branches, and growth in the a direction is accelerated due to enhanced latent heat dissipation. Our observations clearly indicate that the fcIBP occupies a separate position in the classification of IBPs due to the fact that it suppresses the growth of basal faces, despite its moderate freezing point depression.

scholarly journals In vitro uses of biological cryoprotectants

2002 ◽  
Vol 357 (1423) ◽  
pp. 945-951 ◽  
Author(s):  
Peter J. Lillford ◽  
Chris B. Holt
Keyword(s):  
Crystal Growth ◽  
Freezing Point ◽  
Ice Nucleation ◽  
Active Species ◽  
Osmotic Regulation ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Commercial Use ◽  
Crystal Growth Inhibition

Ice can be anything from a highly destructive agent in agriculture to a useful building material. Established industries are based on the known rules of physics and chemistry which allow some control of amounts of ice or ice crystal geometry. However, organisms have much more subtle requirements to maintain their delicate internal structure if they are to survive freezing. As a result they have selected specific molecules for freezing–point depression, osmotic regulation, ice nucleation and crystal growth inhibition. All these active species may have potential commercial use once they are identified, understood and produced at economic scales. We examine the progress made so far in extending biological subtlety into commercial processes, and look for prospects for further innovation.

scholarly journals Modeling interfacial liquid layers on environmental ices

2011 ◽  
Vol 11 (18) ◽  
pp. 9971-9982 ◽  
Author(s):  
M. H. Kuo ◽  
S. G. Moussa ◽  
V. F. McNeill
Keyword(s):  
Gas Phase ◽  
Atmospheric Chemistry ◽  
Low Temperatures ◽  
Freezing Point ◽  
Triple Junctions ◽  
Ice Crystal ◽  
Freezing Point Depression ◽  
Chemical Interactions ◽  
Interfacial Layers ◽  
Wide Range

Abstract. Interfacial layers on ice significantly influence air-ice chemical interactions. In solute-containing aqueous systems, a liquid brine may form upon freezing due to the exclusion of impurities from the ice crystal lattice coupled with freezing point depression in the concentrated brine. The brine may be segregated to the air-ice interface where it creates a surface layer, in micropockets, or at grain boundaries or triple junctions. We present a model for brines and their associated liquid layers in environmental ice systems that is valid over a wide range of temperatures and solute concentrations. The model is derived from fundamental equlibrium thermodynamics and takes into account nonideal solution behavior in the brine, partitioning of the solute into the ice matrix, and equilibration between the brine and the gas phase for volatile solutes. We find that these phenomena are important to consider when modeling brines in environmental ices, especially at low temperatures. We demonstrate its application for environmentally important volatile and nonvolatile solutes including NaCl, HCl, and HNO3. The model is compared to existing models and experimental data from literature where available. We also identify environmentally relevant regimes where brine is not predicted to exist, but the QLL may significantly impact air-ice chemical interactions. This model can be used to improve the representation of air-ice chemical interactions in polar atmospheric chemistry models.

scholarly journals Carrot ‘antifreeze’ protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization

2020 ◽  
Vol 477 (12) ◽  
pp. 2179-2192 ◽  
Author(s):  
Yannan Wang ◽  
Laurie A. Graham ◽  
Zhifu Han ◽  
Robert Eves ◽  
Audrey K. Gruneberg ◽  
...  
Keyword(s):  
Convex Surface ◽  
Freezing Point ◽  
Protein Structures ◽  
Freeze Tolerance ◽  
Antifreeze Protein ◽  
Site Directed Mutagenesis ◽  
Freezing Point Depression ◽  
Freezing Damage ◽  
Ice Recrystallization ◽  
Ice Binding

Ice-binding proteins (IBPs) are found in many biological kingdoms where they protect organisms from freezing damage as antifreeze agents or inhibitors of ice recrystallization. Here, the crystal structure of recombinant IBP from carrot (Daucus carota) has been solved to a resolution of 2.3 Å. As predicted, the protein is a structural homologue of a plant polygalacturonase-inhibiting protein forming a curved solenoid structure with a leucine-rich repeat motif. Unexpectedly, close examination of its surface did not reveal any large regions of flat, regularly spaced hydrophobic residues that characterize the ice-binding sites (IBSs) of potent antifreeze proteins from freeze-resistant fish and insects. An IBS was defined by site-directed mutagenesis of residues on the convex surface of the carrot solenoid. This imperfect site is reminiscent of the irregular IBS of grass ‘antifreeze’ protein. Like the grass protein, the carrot IBP has weak freezing point depression activity but is extremely active at nanomolar concentrations in inhibiting ice recrystallization. Ice crystals formed in the presence of both plant proteins grow slowly and evenly in all directions. We suggest that this slow, controlled ice growth is desirable for freeze tolerance. The fact that two plant IBPs have evolved very different protein structures to affect ice in a similar manner suggests this pattern of weak freezing point depression and strong ice recrystallization inhibition helps their host to tolerate freezing rather than to resist it.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 758-766 ◽  
Author(s):  
Ritu Kapila ◽  
Sandip Das ◽  
Malathi Lakshmikumaran ◽  
P. S. Srivastava
Keyword(s):  
Tandem Repeat ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Consensus Sequence ◽  
Repeat Element ◽  
Matrix Analysis ◽  
Repetitive Region ◽  
Repeat Family ◽  
Sinapis Arvensis ◽  
Species Specific

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5′-TTTAGGG-3′. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature. Key words : Brassica species, Sinapis arvensis, tandem repeats, telomeres.

Deoxyribonucleic Acid as a Tool for Digital Information Storage: An Overview

2019 ◽  
Vol 15 (01) ◽  
pp. 1-8
Author(s):  
Ashish C Patel ◽  
C G Joshi
Keyword(s):  
Data Storage ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Random Access ◽  
Information Storage ◽  
Digital Data ◽  
Digital Information ◽  
Multiple Sequence ◽  
Digital World ◽  
Digital File

Current data storage technologies cannot keep pace longer with exponentially growing amounts of data through the extensive use of social networking photos and media, etc. The "digital world” with 4.4 zettabytes in 2013 has predicted it to reach 44 zettabytes by 2020. From the past 30 years, scientists and researchers have been trying to develop a robust way of storing data on a medium which is dense and ever-lasting and found DNA as the most promising storage medium. Unlike existing storage devices, DNA requires no maintenance, except the need to store at a cool and dark place. DNA has a small size with high density; just 1 gram of dry DNA can store about 455 exabytes of data. DNA stores the informations using four bases, viz., A, T, G, and C, while CDs, hard disks and other devices stores the information using 0’s and 1’s on the spiral tracks. In the DNA based storage, after binarization of digital file into the binary codes, encoding and decoding are important steps in DNA based storage system. Once the digital file is encoded, the next step is to synthesize arbitrary single-strand DNA sequences and that can be stored in the deep freeze until use.When there is a need for information to be recovered, it can be done using DNA sequencing. New generation sequencing (NGS) capable of producing sequences with very high throughput at a much lower cost about less than 0.1 USD for one MB of data than the first sequencing technologies. Post-sequencing processing includes alignment of all reads using multiple sequence alignment (MSA) algorithms to obtain different consensus sequences. The consensus sequence is decoded as the reversal of the encoding process. Most prior DNA data storage efforts sequenced and decoded the entire amount of stored digital information with no random access, but nowadays it has become possible to extract selective files (e.g., retrieving only required image from a collection) from a DNA pool using PCR-based random access. Various scientists successfully stored up to 110 zettabytes data in one gram of DNA. In the future, with an efficient encoding, error corrections, cheaper DNA synthesis,and sequencing, DNA based storage will become a practical solution for storage of exponentially growing digital data.

Depression of freezing temperature of water and water solutions in porous materials

1989 ◽  
Vol 54 (10) ◽  
pp. 2644-2647 ◽  
Author(s):  
Petr Schneider ◽  
Jiří Rathouský
Keyword(s):  
Water Vapor ◽  
Porous Materials ◽  
Inorganic Salt ◽  
Freezing Point ◽  
Freezing Temperature ◽  
Inorganic Salts ◽  
Freezing Point Depression ◽  
Salt Solutions ◽  
Water Solutions

In porous materials filled with water or water solutions of inorganic salts, water freezes at lower temperatures than under normal conditions; the reason is the decrease of water vapor tension above the convex meniscus of liquid in pores. The freezing point depression is not very significant in pores with radii from 0.05 μm to 10 μm (about 0.01-2.5 K). Only in smaller pores, especially when filled with inorganic salt solutions, this depression is important.

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