A brief review of applications of antifreeze proteins in cryopreservation and metabolic genetic engineering

Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants

Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four α-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures.

Frost fighters: unveiling the potential of microbial antifreeze proteins in biotech innovation

Polar environments pose extreme challenges for life due to low temperatures, limited water, high radiation, and frozen landscapes. Despite these harsh conditions, numerous macro and microorganisms have developed adaptive strategies to reduce the detrimental effects of extreme cold. A primary survival tactic involves avoiding or tolerating intra and extracellular freezing. Many organisms achieve this by maintaining a supercooled state by producing small organic compounds like sugars, glycerol, and amino acids, or through increasing solute concentration. Another approach is the synthesis of ice-binding proteins, specifically antifreeze proteins (AFPs), which hinder ice crystal growth below the melting point. This adaptation is crucial for preventing intracellular ice formation, which could be lethal, and ensuring the presence of liquid water around cells. AFPs have independently evolved in different species, exhibiting distinct thermal hysteresis and ice structuring properties. Beyond their ecological role, AFPs have garnered significant attention in biotechnology for potential applications in the food, agriculture, and pharmaceutical industries. This review aims to offer a thorough insight into the activity and impacts of AFPs on water, examining their significance in cold-adapted organisms, and exploring the diversity of microbial AFPs. Using a meta-analysis from cultivation-based and cultivation-independent data, we evaluate the correlation between AFP-producing microorganisms and cold environments. We also explore small and large-scale biotechnological applications of AFPs, providing a perspective for future research.

Polyvinyl alcohol addition to freezing extender can improve the post-thaw quality, longevity and in vitro fertility of ram epididymal spermatozoa

Recovering and cryopreserving epididymal spermatozoa are suitable methods for preserving the genetic potential of livestock and endangered species. Regarding encouraging reports on the use of polyvinyl alcohol (PVA) in cryopreserving various cell types, we conducted this study to examine the impact of PVA on the post-thaw quality, longevity, and in vitro fertility of ram epididymal sperm. In the first experiment, ram epididymal spermatozoa were frozen in extenders containing 6 % glycerol and 0, 0.5, 1, 2, 5, 10, or 15 mg/ml of PVA. Polyvinyl alcohol at concentrations of 0.5, 1, and 2 mg/ml improved the motility and functional membrane integrity (FMI) of the sperm compared with the control group (P < 0.05). In the second experiment, we investigated whether PVA could partially substitute glycerol in the freezing extender. PVA was added at 0, 0.5, 1, and 2 mg/ml to the extenders containing 1 % or 2 % glycerol. After thawing, the sperm motility parameters of the group containing 1 mg/ml PVA and 2 % glycerol were significantly higher than those of the un-supplemented groups (P < 0.05). In the third experiment, the effect of PVA on the post-thaw sperm longevity were examined. Sperm were frozen in 3 extenders: one containing 6 % glycerol and 1 mg/ml PVA (Gly6P1), another containing 2 % glycerol and 1 mg/ml PVA (Gly2P1), and a control extender with 6 % glycerol. After thawing, the quality of the sperm was evaluated. Sperm were then diluted in human tubal fluid (HTF) and incubated at 37 °C for 3 h. Afterwards, the quality of the sperm was evaluated once more. The presence of PVA in the freezing extender improved motility parameters and FMI. Additionally, PVA-containing groups had lower proportions of capacitated and acrosome reacted sperm compared with the control group (P < 0.05). The Gly6P1 group performed better than the other two groups (P < 0.05). In the fourth experiment, sperm from the Gly6P1 and Control groups were used in the IVF process immediately after thawing (T0) and after a 3-h incubation at 37 °C in HTF (T3). Cleavage, blastocyst and hatching rates in both groups were similar at T0, but they were lower in the Control group at T3 (P < 0.05). In conclusion, PVA as an additive to the freezing extender significantly improves post-thaw motility, viability, acrosome integrity, longevity, and fertile lifespan of ram epididymal spermatozoa.

Computational Design of Peptides for Biomaterials Applications

Computer-aided molecular design and protein engineering emerge as promising and active subjects in bioengineering and biotechnological applications. On one hand, due to the advancing computing power in the past decade, modeling toolkits and force fields have been put to use for accurate multiscale modeling of biomolecules including lipid, protein, carbohydrate, and nucleic acids. On the other hand, machine learning emerges as a revolutionary data analysis tool that promises to leverage physicochemical properties and structural information obtained from modeling in order to build quantitative protein structure-function relationships. We review recent computational works that utilize state-of-the-art computational methods to engineer peptides and proteins for various emerging biomedical, antimicrobial, and antifreeze applications. We also discuss challenges and possible future directions toward developing a roadmap for efficient biomolecular design and engineering.

Novel Apoplastic Antifreeze Proteins of Deschampsia antarctica as Enhancer of Common Cell Freezing Media for Cryobanking of Genetic Resources, a Preliminary Study

Antifreeze proteins (AFPs) are natural biomolecules found in cold-adapted organisms that lower the freezing point of water, allowing survival in icy conditions. These proteins have the potential to improve cryopreservation techniques by enhancing the quality of genetic material postthaw. Deschampsia antarctica, a freezing-tolerant plant, possesses AFPs and is a promising candidate for cryopreservation applications. In this study, we investigated the cryoprotective properties of AFPs from D. antarctica extracts on Atlantic salmon spermatozoa. Apoplastic extracts were used to determine ice recrystallization inhibition (IRI), thermal hysteresis (TH) activities and ice crystal morphology. Spermatozoa were cryopreserved using a standard cryoprotectant medium (C+) and three alternative media supplemented with apoplastic extracts. Flow cytometry was employed to measure plasma membrane integrity (PMI) and mitochondrial membrane potential (MMP) postthaw. Results showed that a low concentration of AFPs (0.05 mg/mL) provided significant IRI activity. Apoplastic extracts from D. antarctica demonstrated a cryoprotective effect on salmon spermatozoa, with PMI comparable to the standard medium. Moreover, samples treated with apoplastic extracts exhibited a higher percentage of cells with high MMP. These findings represent the first and preliminary report that suggests that AFPs derived from apoplastic extracts of D. antarctica have the potential to serve as cryoprotectants and could allow the development of novel freezing media.

Accurate Prediction of Antifreeze Protein from Sequences through Natural Language Text Processing and Interpretable Machine Learning Approaches

Antifreeze proteins (AFPs) bind to growing iceplanes owing to their structural complementarity nature, thereby inhibiting the ice-crystal growth by thermal hysteresis. Classification of AFPs from sequence is a difficult task due to their low sequence similarity, and therefore, the usual sequence similarity algorithms, like Blast and PSI-Blast, are not efficient. Here, a method combining n-gram feature vectors and machine learning models to accelerate the identification of potential AFPs from sequences is proposed. All these n-gram features are extracted from the K-mer counting method. The comparative analysis reveals that, among different machine learning models, Xgboost outperforms others in predicting AFPs from sequence when penta-mers are used as a feature vector. When tested on an independent dataset, our method performed better compared to other existing ones with sensitivity of 97.50%, recall of 98.30%, and f1 score of 99.10%. Further, we used the SHAP method, which provides important insight into the functional activity of AFPs.

Engulfment Avalanches and Thermal Hysteresis for Antifreeze Proteins on Supercooled Ice

Antifreeze proteins (AFPs) bind to the ice-water surface and prevent ice growth at temperatures below 0 °C through a Gibbs-Thomson effect. Each adsorbed AFP creates a metastable depression on the surface that locally resists ice growth, until ice engulfs the AFP. We recently predicted the susceptibility to engulfment as a function of AFP size, distance between AFPs, and supercooling [ J. Chem. Phys. 2023, 158, 094501]. For an ensemble of AFPs adsorbed on the ice surface, the most isolated AFPs are the most susceptible, and when an isolated AFP gets engulfed, its former neighbors become more isolated and more susceptible to engulfment. Thus, an initial engulfment event can trigger an avalanche of subsequent engulfment events, leading to a sudden surge of unrestrained ice growth. This work develops a model to predict the supercooling at which the first engulfment event will occur for an ensemble of randomly distributed AFP pinning sites on an ice surface. Specifically, we formulate an inhomogeneous survival probability that accounts for the AFP coverage, the distribution of AFP neighbor distances, the resulting ensemble of engulfment rates, the ice surface area, and the cooling rate. We use the model to predict thermal hysteresis trends and compare with experimental data.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Virology under the Microscope-a Call for Rational Discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Hayvanlarda Soğuğa Dayanıklılık: Çift Yaşarların Kriyobiyolojisi

Organizmalar yaşamlarını devam ettirebilmek için abiyotik çevresel koşullara uyum sağlarlar. Özellikle ortam sıcaklığındaki değişimler; canlıların beslenme, üreme, gelişim ve morfolojileri üzerinde etkilidir. Sıra dışı sıcaklık değişimleri özellikle ektotermik hayvanlar için ölümcül olabilir. Karasal ektotermler. doğada donma noktasının altındaki sıcaklıklarda hayatta kalabilmek için davranışsal, fizyolojik ve biyokimyasal bazı özel stratejiler geliştirmişlerdir. Bazı türler göç ederek su ya da toprak altında kış uykusuna yatmak suretiyle dondurucu sıcaklıklardan kaçınırlar. Bazıları ise donma koşullarına maruz kalarak kışı geçirmek zorundadırlar. Genel olarak dondurucu soğuğa dayanıklılık donmadan kaçınma (süper soğuma) ve donma toleransı stratejilerine bağlıdır. Donmadan kaçınma durumunda vücut sıvılarının donma noktasının altındaki sıcaklıklarda sıvı formu korunurken donma toleransı stratejisini kullanan canlılarda ise vücutlarındaki toplam suyun %50’sinden fazlasının donması tolere edilebilir. Karasal hibernatör hayvanlardan bazı amfibi ve sürüngen gruplarında da tespit edilen donma toleransı stratejisi onların dondurucu kış koşullarında hayatta kalmalarını sağlamaktadır. Bu özel türler kriyoprotektif mekanizmaları ile donmanın ölümcül etkilerinden korunurlar. Donma süresince yaşamsal faaliyetleri tamamen duran bu hayvanlar çözündükten sonra kısa bir süre içerisinde de normal yaşama dönerler. Bu mucizevi mekanizmanın araştırılması yalnızca hayvanların karmaşık adaptasyonunu açıklamakla kalmaz, aynı zamanda doku ve hücre kriyoprezervasyon teknolojisine de kaynak sağlar. Bu derleme amfibilerin donma toleransı stratejilerine dair bilgiler sunarak henüz yeterince çalışılmamış bu konuda araştırma yapmak isteyenlere katkı sağlayacaktır.

Polysaccharide-Derived Ice Recrystallization Inhibitors with a Modular Design: The Case of Dextran-Based Graft Polymers

Ice recrystallization inhibitors inspired from antifreeze proteins (AFPs) are receiving increasing interest for cryobiology and other extreme environment applications. Here, we present a modular strategy to develop polysaccharide-derived biomimetics, and detailed studies were performed in the case of dextran. Poly(vinyl alcohol) (PVA) which has been termed as one of the most potent biomimetics of AFPs was grafted onto dextran via thiol-ene click chemistry (Dex-g-PVA). This demonstrated that Dex-g-PVA is effective in IRI and its activity increases with the degree of polymerization (DP) (sizes of ice crystals were 18.846 ± 1.759 and 9.700 ± 1.920 μm with DPs of 30 and 80, respectively) and fraction of PVA. By means of the dynamic ice shaping (DIS) assay, Dex-g-PVA is found to engage on the ice crystal surfaces, thus the ice affinity accounts for their IRI activity. In addition, Dex- g-PVA displayed enhanced IRI activity compared to that of equivalent PVA alone. We speculate that the hydrophilic nature of dextran would derive PVA in a stretch conformation that favors ice binding. The modular design can not only offer polysaccharides IRI activity but also favor the ice-binding behavior of PVA.

Bioinspired Freeze-Tolerant Soft Materials: Design, Properties, and Applications

In nature, many biological organisms have developed the exceptional antifreezing ability to survive in extremely cold environments. Inspired by the freeze resistance of these organisms, researchers have devoted extensive efforts to develop advanced freeze-tolerant soft materials and explore their potential applications in diverse areas such as electronic skin, soft robotics, flexible energy, and biological science. Herein, a comprehensive overview on the recent advancement of freeze-tolerant soft materials and their emerging applications from the perspective of bioinspiration and advanced material engineering is provided. First, the mechanisms underlying the freeze tolerance of cold-enduring biological organisms are introduced. Then, engineering strategies for developing antifreezing soft materials are summarized. Thereafter, recent advances in freeze-tolerant soft materials for different technological applications such as smart sensors and actuators, energy harvesting and storage, and cryogenic medical applications are presented. Finally, future challenges and opportunities for the rapid development of bioinspired freeze-tolerant soft materials are discussed.

Bioinspired Ice-Binding Materials for Tissue and Organ Cryopreservation

Cryopreservation of tissues and organs can bring transformative changes to medicine and medical science. In the past decades, limited progress has been achieved, although cryopreservation of tissues and organs has long been intensively pursued. One key reason is that the cryoprotective agents (CPAs) currently used for cell cryopreservation cannot effectively preserve tissues and organs because of their cytotoxicity and tissue destructive effect as well as the low efficiency in controlling ice formation. In stark contrast, nature has its unique ways of controlling ice formation, and many living organisms can effectively prevent freezing damage. Ice-binding proteins (IBPs) are regarded as the essential materials identified in these living organisms for regulating ice nucleation and growth. Note that controversial results have been reported on the utilization of IBPs and their mimics for the cryopreservation of tissues and organs, that is, some groups revealed that IBPs and mimics exhibited unique superiorities in tissues cryopreservation, while other groups showed detrimental effects. In this perspective, we analyze possible reasons for the controversy and predict future research directions in the design and construction of IBP inspired ice-binding materials to be used as new CPAs for tissue cryopreservation after briefly introducing the cryo-injuries and the challenges of conventional CPAs in the cryopreservation of tissues and organs.

Antifreeze Proteins: Novel Applications and Navigation towards Their Clinical Application in Cryobanking

Antifreeze proteins (AFPs) or thermal hysteresis (TH) proteins are biomolecular gifts of nature to sustain life in extremely cold environments. This family of peptides, glycopeptides and proteins produced by diverse organisms including bacteria, yeast, insects and fish act by non-colligatively depressing the freezing temperature of the water below its melting point in a process termed thermal hysteresis which is then responsible for ice crystal equilibrium and inhibition of ice recrystallisation; the major cause of cell dehydration, membrane rupture and subsequent cryodamage. Scientists on the other hand have been exploring various substances as cryoprotectants. Some of the cryoprotectants in use include trehalose, dimethyl sulfoxide (DMSO), ethylene glycol (EG), sucrose, propylene glycol (PG) and glycerol but their extensive application is limited mostly by toxicity, thus fueling the quest for better cryoprotectants. Hence, extracting or synthesizing antifreeze protein and testing their cryoprotective activity has become a popular topic among researchers. Research concerning AFPs encompasses lots of effort ranging from understanding their sources and mechanism of action, extraction and purification/synthesis to structural elucidation with the aim of achieving better outcomes in cryopreservation. This review explores the potential clinical application of AFPs in the cryopreservation of different cells, tissues and organs. Here, we discuss novel approaches, identify research gaps and propose future research directions in the application of AFPs based on recent studies with the aim of achieving successful clinical and commercial use of AFPs in the future.

Review: The case for studying mitochondrial function during plant cryopreservation

Cryopreservation has several advantages over other ex situ conservation methods, and indeed is the only viable storage method for the long term conservation of most plant species. However, despite many advances in this field, it is increasingly clear that some species are ill-equipped to overcome the intense stress imposed by the cryopreservation process, making protocol development incredibly difficult using traditional trial and error methods. Cryobiotechnology approaches have been recently recognised as a strategic way forward, utilising intimate understanding of biological systems to inform development of more effective cryopreservation protocols. Mitochondrial function is a model candidate for a cryobiotechnological approach, as it underpins not only energy provision, but also several other key determinants of germplasm outcome, including stress response, reduction-oxidation status, and programmed cell death. Extensive research in animal cell and tissue cryopreservation has established a clear link between mitochondrial health and cryopreservation survival, but also indicates that mitochondria are routinely subject to damage from multiple aspects of the cryopreservation process. Evidence is already emerging that mitochondrial dysfunction may also occur in plant cryopreservation, and this research can be greatly expanded by using considered applications of innovative technologies. A range of mitochondria-targeted prophylactic and therapeutic interventions already exist with potential to improve cryopreservation outcomes through mitochondrial function.

Recent development in evaluation methods, influencing factors and control measures for freeze denaturation of food protein

Frozen storage is most widely adopted preservation method to maintain food freshness and nutritional attributes. However, at low temperature, food is prone to chemical changes such as protein denaturation and lipid oxidation. In this review, we discussed the reasons and influencing factors that cause protein denaturation during freezing, such as freezing rate, freezing temperature, freezing method, etc. From the previous literatures, it was found that frozen storage is commonly used to prevent freeze induced protein denaturation by adding cryoprotectants to food. Some widely used cryoprotectants (for example, sucrose and sorbitol) have been reported with higher sweetness and weaker cryoprotective abilities. Therefore, this article comprehensively discusses the new cryopreservation methods and providing comparative study to the conventional frozen storage. Meanwhile, this article sheds light on the freeze induced alterations, such as change in functional and gelling properties. In addition, this article could be helpful for the prolonged frozen storage of food with minimum quality related changes. Meanwhile, it could also improve the commercial values and consumer satisfaction of frozen food as well.

Bioinspired Crowding Inhibits Explosive Ice Growth in Antifreeze Protein Solutions

Antifreeze (glyco)proteins (AF(G)Ps) are naturally evolved ice inhibitors incomparable to any man-made materials, thus, they are gaining intensive interest for cryopreservation and beyond. AF(G)Ps depress the freezing temperature (T_f) noncolligatively below the melting temperature (T_m), generating a thermal hysteresis (TH) gap, within which the ice growth is arrested. However, the ice crystals have been reported to undergo a retaliatory and explosive growth beyond the TH gap, which is lethal to living organisms. Although intensive research has been carried to inhibit such an explosive ice growth, no satisfactory strategy has been discovered until now. Here, we report that crowded solutions mimicking an extracellular matrix (ECM), in which AF(G)Ps are located, can completely inhibit the explosive ice growth. The crowded solutions are the condensates of liquid-liquid phase separation consisting of polyethylene glycol (PEG) and sodium citrate (SC), which possess a nanoscale network and strong hydrogen bond (HB) forming ability, completely different to crowded solutions made of single components, that is, PEG or SC. Due to these unique features, the dynamics of the water is significantly slowed down, and the energy needed for breaking the HB between water molecules is distinctly increased; consequently, ice growth is inhibited as the rate of water molecules joining the ice is substantially reduced. The present work not only opens a new avenue for cryopreservation, but also suggests that the ECM of cold-hardy organisms, which also exhibit great water confining properties, may have a positive effect in protecting the living organisms from freezing damage.

Antifreeze Protein Improves the Cryopreservation Efficiency of Hosta capitata by Regulating the Genes Involved in the Low-Temperature Tolerance Mechanism

In this study, whether the addition of antifreeze protein (AFP) to a cryopreservative solution (plant vitrification solution 2 (PVS2)) is more effective in reducing freezing injuries in Hosta capitata than PVS2 alone at different cold exposure times (6, 24, and 48 h) is investigated. The upregulation of C-repeat binding factor 1 (CBF1) and dehydrin 1 (DHN1) in response to low temperature was observed in shoots. Shoots treated with distilled water (dH2O) strongly triggered gene expression 6 h after cold exposure, which was higher than those expressed in PVS2 and PVS2+AFP. However, 24 h after cold exposure, gene expressions detected in dH2O and PVS2 treatments were similar and higher than PVS2 + AFP. The expression was highest in PVS2+AFP when the exposure time was extended to 48 h. Similarly, nitric reductase activities 1 and 2 (Nia1 and Nia2) genes, which are responsible for nitric oxide production, were also upregulated in low-temperature-treated shoots, as observed for CBF1 and DHN1 expression patterns during cold exposure periods. Based on the gene expression patterns, shoots treated with PVS2+AFP were more likely to resist cold stress, which was also associated with the higher cryopreservation efficiency of PVS2+AFP compared to PVS2 alone. This finding suggests that the improvement of cryopreservation efficiency by AFP could be due to the transcriptional regulation of CBF1, DHN1, Nia1, and Nia2, which might reduce freezing injuries during cryopreservation. Thus, AFP could be potentially used as a cryoprotectant in the cryopreservation of rare and commercially important plant germplasm.

Cryopreservation of plant cell cultures - Diverse practices and protocols

Plant cell cultures can be used as biotechnological platforms for the commercial production of small-molecule active ingredients and recombinant proteins, such as biopharmaceuticals. This requires the cryopreservation of well-characterized cell lines as master cell banks from which uniform working cell banks can be derived to ensure high batch-to-batch reproducibility during production campaigns. However, the cryopreservation of plant cells is challenging due to their low viability and poor regrowth after thawing. Three approaches have been developed: slow freezing, vitrification, and encapsulation-dehydration. Typically, the protocols are iteratively adapted to accommodate the properties of different plant cell lines, taking time and resources while achieving moderate success. Since standardized processes are a prerequisite for industrial applications, this review presents an in-depth analysis of the different procedures for cryopreservation of plant suspension cell cultures, highlighting relevant parameters for effective cryopreservation and the re-establishment of vigorous plant cell cultures within weeks. The protocol variants are grouped into modules that facilitate the directed improvement of each step and allow protocol evolution by module recombination. Ultimately, such improved cryopreservation protocols will form the basis of processes that comply with good manufacturing practice and attract major biopharmaceutical companies to the benefits of plant molecular farming.

Towards a method for cryopreservation of mosquito vectors of human pathogens

Mosquito-borne diseases are responsible for millions of human deaths every year, posing a massive burden on global public health. Mosquitoes transmit a variety of bacteria, parasites and viruses. Mosquito control efforts such as insecticide spraying can reduce mosquito populations, but they must be sustained in order to have long term impacts, can result in the evolution of insecticide resistance, are costly, and can have adverse human and environmental effects. Technological advances have allowed genetic manipulation of mosquitoes, including generation of those that are still susceptible to insecticides, which has greatly increased the number of mosquito strains and lines available to the scientific research community. This generates an associated challenge, because rearing and maintaining unique mosquito lines requires time, money and facilities, and long-term maintenance can lead to adaptation to specific laboratory conditions, resulting in mosquito lines that are distinct from their wild-type counterparts. Additionally, continuous rearing of transgenic lines can lead to loss of genetic markers, genes and/or phenotypes. Cryopreservation of valuable mosquito lines could help circumvent these limitations and allow researchers to reduce the cost of rearing multiple lines simultaneously, maintain low passage number transgenic mosquitoes, and bank lines not currently being used. Additionally, mosquito cryopreservation could allow researchers to access the same mosquito lines, limiting the impact of unique laboratory or field conditions. Successful cryopreservation of mosquitoes would expand the field of mosquito research and could ultimately lead to advances that would reduce the burden of mosquito-borne diseases, possibly through rear-and-release strategies to overcome mosquito insecticide resistance. Cryopreservation techniques have been developed for some insect groups, including but not limited to fruit flies, silkworms and other moth species, and honeybees. Recent advances within the cryopreservation field, along with success with other insects suggest that cryopreservation of mosquitoes may be a feasible method for preserving valuable scientific and public health resources. In this review, we will provide an overview of basic mosquito biology, the current state of and advances within insect cryopreservation, and a proposed approach toward cryopreservation of Anopheles stephensi mosquitoes.

Brief Overview of Ice Nucleation

The nucleation of ice is vital in cloud physics and impacts on a broad range of matters from the cryopreservation of food, tissues, organs, and stem cells to the prevention of icing on aircraft wings, bridge cables, wind turbines, and other structures. Ice nucleation thus has broad implications in medicine, food engineering, mineralogy, biology, and other fields. Nowadays, the growing threat of global warming has led to intense research activities on the feasibility of artificially modifying clouds to shift the Earth’s radiation balance. For these reasons, nucleation of ice has been extensively studied over many decades and rightfully so. It is thus not quite possible to cover the whole subject of ice nucleation in a single review. Rather, this feature article provides a brief overview of ice nucleation that focuses on several major outstanding fundamental issues. The author’s wish is to aid early researchers in ice nucleation and those who wish to get into the field of ice nucleation from other disciplines by concisely summarizing the outstanding issues in this important field. Two unresolved challenges stood out from the review, namely the lack of a molecular-level picture of ice nucleation at an interface and the limitations of classical nucleation theory.

AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs

Species living in extremely cold environments resist the freezing conditions through antifreeze proteins (AFPs). Apart from being essential proteins for various organisms living in sub-zero temperatures, AFPs have numerous applications in different industries. They possess very small resemblance to each other and cannot be easily identified using simple search algorithms such as BLAST and PSI-BLAST. Diverse AFPs found in fishes (Type I, II, III, IV and antifreeze glycoproteins (AFGPs)), are sub-types and show low sequence and structural similarity, making their accurate prediction challenging. Although several machine-learning methods have been proposed for the classification of AFPs, prediction methods that have greater reliability are required. In this paper, we propose a novel machine-learning-based approach for the prediction of AFP sequences using latent space learning through a deep auto-encoder method. For latent space pruning, we use the output of the auto-encoder with a deep neural network classifier to learn the non-linear mapping of the protein sequence descriptor and class label. The proposed method outperformed the existing methods, yielding excellent results in comparison. A comprehensive ablation study is performed, and the proposed method is evaluated in terms of widely used performance measures. In particular, the proposed method demonstrated a high Matthews correlation coefficient of 0.52, F-score of 0.49, and Youden’s index of 0.81 on an independent test dataset, thereby outperforming the existing methods for AFP prediction.

Identifying Antifreeze Proteins Based on Key Evolutionary Information

Antifreeze proteins are important antifreeze materials that have been widely used in industry, including in cryopreservation, de-icing, and food storage applications. However, the quantity of some commercially produced antifreeze proteins is insufficient for large-scale industrial applications. Further, many antifreeze proteins have properties such as cytotoxicity, severely hindering their applications. Understanding the mechanisms underlying the protein-ice interactions and identifying novel antifreeze proteins are, therefore, urgently needed. In this study, to uncover the mechanisms underlying protein-ice interactions and provide an efficient and accurate tool for identifying antifreeze proteins, we assessed various evolutionary features based on position-specific scoring matrices (PSSMs) and evaluated their importance for discriminating of antifreeze and non-antifreeze proteins. We then parsimoniously selected seven key features with the highest importance. We found that the selected features showed opposite tendencies (regarding the conservation of certain amino acids) between antifreeze and non-antifreeze proteins. Five out of the seven features had relatively high contributions to the discrimination of antifreeze and non-antifreeze proteins, as revealed by a principal component analysis, i.e., the conservation of the replacement of Cys, Trp, and Gly in antifreeze proteins by Ala, Met, and Ala, respectively, in the related proteins, and the conservation of the replacement of Arg in non-antifreeze proteins by Ser and Arg in the related proteins. Based on the seven parsimoniously selected key features, we established a classifier using support vector machine, which outperformed the state-of-the-art tools. These results suggest that understanding evolutionary information is crucial to designing accurate automated methods for discriminating antifreeze and non-antifreeze proteins. Our classifier, therefore, is an efficient tool for annotating new proteins with antifreeze functions based on sequence information and can facilitate their application in industry.

Tomato seeds pretreated with Antifreeze protein type I (AFP I) promotes the germination under cold stress by regulating the genes involved in germination process

This study was conducted to investigate the involvement of antifreeze proteins (AFPs; type I and III) in the germination mechanism of tomato seeds under low temperature stress. Germination of the seeds grown at a room temperature (25°C) was observed on 5 days after sowing (DAS), while all seeds exposed to a low temperature started to germinate at 16 days after sowing (DAS). However, in comparison with control seeds (0 µg/l), seeds treated with AFP I (100, 300, or 500 µg/l) germinated earlier and at a higher percentage until 20 DAS, and seeds treated with 100 µg/l AFP I showed the highest percentage of germination. Surprisingly, AFP III did not significantly increase germination, and the rate was lower among 500 µg/l AFP III-treated seeds compared with control seeds (0 µg/l). The transcription levels of the plasma membrane-associated H⁺-ATPase gene and antioxidant-related superoxide dismutase (SOD) and catalase 1 (CAT1) genes were analyzed, and the transcription levels of the genes in the seeds grown at 25°C were relatively low. For low temperature-treated seeds, H⁺-ATPase in control seeds (0 µg/l) was higher compared with that in AFP I-treated seeds and was lower compared with that in AFP III-treated seeds. The expression levels of the antioxidant-related genes (SOD and CAT1) were lower in AFP I-treated seeds than in control seeds (0 µg/l); however, they were higher in AFP III-treated seeds than in control seeds (0 µg/l). Overall, compared with AFP III, AFP I may potentially function as a cold-protective agent by modulating the genes associated with seed germination.