FBS-based cryoprotective compositions for effective cryopreservation of gut microbiota and key intestinal microorganisms.

OBJECTIVE: The need for innovative techniques to preserve microbiota for extended periods, while maintaining the species composition and quantitative balance of the bacterial community, is becoming increasingly important. To address this need, we propose an efficient approach to cryopreserve human gut microbiota using a two-component cryoprotective composition comprising fetal bovine serum (FBS) and 5% dimethyl sulfoxide (DMSO). Fetal serum is a commonly utilized component in the freezing media for eukaryotic cells, however, its effects on prokaryotic cells have not been extensively researched. RESULTS: In our study, we demonstrated the high efficiency of using a two-component cryoprotective medium, FBS + 5% DMSO, for cryopreservation of human gut microbiota using three different methods. According to the obtained results, the intact donor microbiota was preserved at a level of 85 ± 4% of the initial composition based on fluorescent analysis using the LIVE/DEAD test. No differences in survival were observed when comparing with pure DMSO and FBS media. The photometric measurement method for growth of aerobic bacteria (A. johnsoni), facultative anaerobes (E. coli, E. faecalis), microaerophilic (L. plantarum), and obligate anaerobic bacterial cultures (E. barkeri, B. breve) also demonstrated high viability rates of 94-98% in the two-component protective medium, reaching intact control levels. However, for anaerobic microflora representatives, serum proved to be a more suitable cryoprotectant. Also, we demonstrated that using cryoprotective media with 50-75% FBS content is enough to preserve a significant level of bacterial cell viability, from an economic standpoint.

Prolonged hypothermic storage of oocytes of the European common frog Rana temporaria in a gas mixture of oxygen and carbon monoxide.

The maximum hypothermic storage time of amphibian oocytes is several hours, which is due to the peculiarities of the structure of the cell envelope. The authors of this paper have already demonstrated the possibility of increasing the storage period of unfertilized oocytes of the common frog (Rana temporaria) up to 5-7 days. The aim of the current study was to determine the possibility of using a 6.5 atm gaseous mixture of carbon monoxide and oxygen, for prolonged hypothermic preservation of unfertilized oocytes for 4 to 12 days. After four days, oocytes stored under CO+O2 conditions exhibited fertilization and hatching rates that were 1.6 and 2.2-fold higher than control, respectively. While no oocytes in the control group survived to day twelve, oocytes held under CO +O2 gas exhibited a 39±14% (38 out of 99 oocytes in total) fertilization rate, however only 1±2% (1/99) of those hatched. This approach is promising for the storage of genetic material from female amphibians, particularly in respect to managing and restoring endangered species, but may also be applicable to oocytes of other classes of vertebrates.

Time Limiting Boundaries of Reversible Clinical Death in Rats Subjected to Ultra-Deep Hypothermia.

BACKGROUND: It is well known that body temperature maintenance between 20 and 35°C prevents hypoxic damage. However, data regarding the ideal duration and permissible temperature boundaries for ultra-deep hypothermia below 20°C are rather fragmentary. The aim of the present study was to determine the time limits of reversible clinical death in rats subjected to ultra-deep hypothermia at 1-8°C. RESULTS: Rat survival rates were directly dependent on the duration of clinical death. If clinical death did not exceed 35 min, animal viability could be restored. Extending the duration of clinical death longer than 45 min led to rat death, and cardiac functioning in these animals was not recovered. The rewarming rate and the lowest temperature of hypothermia experienced did not directly influence survival rates. CONCLUSIONS: In a rat model, reversible ultra-deep hypothermia as low as 1-8°C could be achieved without the application of hypercapnia or pharmacological support. The survival of animals was dependent on the duration of clinical death, which should not exceed 35 min.

Influence of helium, xenon, and other noble gases on cryopreservation of Hela and l929 cell lines.

Any biological material contains dissolved gases that affect physical and biological processes associated with cooling and freezing. However, in the cryobiology literature, little attention has been paid to the effect of gasses on cryopreservation. We studied the influence of helium, neon, krypton, xenon, argon, nitrogen, and sulfur hexafluoride on the survivability of HeLa and L929 cell lines during cryopreservation. Saturation of a cell suspension with helium, neon, and sulfur hexafluoride enhanced survival of HeLa and L929 cells after cryopreservation. Helium exerted the most significant effect. For a range of noble gases, the efficiency of the positive effect decreased as the molecular mass of the gas increased. This paper discusses possible mechanisms for the influence of gases on the cryopreservation of biological material. The most probable mechanism is the disruption of the frozen solution structure with gas-filled microbubbles produced during water crystallization. Ultimately, it was concluded that helium and neon can be used to improve methods for cryopreservation of cell suspensions with a low concentration of conventional penetrating cryoprotectants or even without them.

Cryopreservation of the human gut microbiota: Current state and perspectives.

The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.

A Study of the Effect of a Protein on the Structure of Water in Solution Using Terahertz Time-Domain Spectroscopy.

Terahertz time-domain spectroscopy (THz-TDS) was used to determine the spectra (range = 1.2-120 cm-1) of aqueous solutions of bovine serum albumin (BSA) at pH range 2.5-10. Under each of the selected pH, BSA molecules exist in a different conformation, compared to other pH values. The spectra were used to calculate the functions of the dielectric permittivity of BSA solutions. Dielectric functions of the aqueous phase of BSA solutions were calculated based on the Bruggeman model, without the contribution of BSA itself. Fitting of the dielectric functions was performed using a model which includes three water spectral bands: two relaxation bands with relaxation times of about 8.28 and 0.3 ps and a vibrational band with a maximum of about 180 cm-1. The parameters of these bands were determined through fitting and physical interpretation at the molecular level can be provided for each of them. A comparison between the values of model parameters of solutions with BSA and without BSA allowed to conclude that the main effect of BSA is the formation of strongly bound hydration shells in the immediate proximity to the protein molecule. At the same time, the structure of more distant layers of the hydration shells is destroyed, with an increased formation of free water molecules. Some differences are observed in the effect of different BSA conformations on the aqueous phase of solution. The proposed approach can be generalized and applied for studying of a wide class of biological macromolecules in aqueous solutions.

Extremely low-level microwaves attenuate immune imbalance induced by inhalation exposure to low-level toluene in mice.

PURPOSE: To clarify whether extremely low-level microwaves (MW) alone or in combination with p38 inhibitor affect immune cell responses to inhalation exposure of mice to low-level toluene. MATERIALS AND METHODS: The cytokine profile, heat shock proteins expression, and the activity of several signal cascades, namely, NF-κB, SAPK/JNK, IRF-3, p38 MAPK, and TLR4 were measured in spleen lymphocytes of mice treated to air-delivered toluene (0.6 mg/m3) or extremely low-level microwaves (8.15-18 GHz, 1µW/cm2, 1 Hz swinging frequency) or combined action of these two factors. RESULTS: A single exposure to air-delivered low-level toluene induced activation of NF-κB, SAPK/JNK, IFR-3, p38 MAPK and TLR4 pathways. Furthermore, air toluene induced the expression of Hsp72 and enhanced IL-1, IL-6, and TNF-α in blood plasma, which is indicative of a pro-inflammatory response. Exposure to MW alone also resulted in the enhancement of the plasma cytokine values (e.g. IL-6, TNF-α, and IFN-γ) and activation of the NF-κB, MAPK p38, and especially the TLR4 pathways in splenic lymphocytes. Paradoxically, pre-exposure to MW partially recovered or normalized the lymphocyte parameters in the toluene-exposed mice, while the p38 inhibitor XI additionally increased protective activity of microwaves by down regulating MAPKs (JNK and p38), IKK, as well as expression of TLR4 and Hsp90-α. CONCLUSIONS: The results suggest that exposure to low-intensity MW at specific conditions may recover immune parameters in mice undergoing inhalation exposure to low-level toluene via mechanisms involving cellular signaling.

Terahertz Spectroscopy Applied for Investigation of Water Structure.

The absorption spectra of liquid water and various aqueous solutions were analyzed in a terahertz frequency domain (from 6 to 200 cm(-1)) which characterize the collective dynamics of water molecules. Particular attention was paid to the relaxation process in the range of ∼6-80 cm(-1). The physical essence of this process on the molecular level is still unclear. We found that the amplitude of this relaxation process correlates with the degree of destruction of water structure. The obtained data allowed us to interpret this process as a monomolecular relaxation of free water molecules. On the basis of a consideration of the water polarization in the electric field, we proposed a method of calculation of the amount of free water molecules in solution.

The role of the NF-κB, SAPK/JNK, and TLR4 signalling pathways in the responses of RAW 264.7 cells to extremely low-intensity microwaves.

PURPOSE: To investigate the role of the toll-like receptor 4 (TLR4), nuclear factor κB (NF-κB), and stress activated protein kinases/Jun N-terminal kinase (SAPK/JNK) signalling pathways in the responses of RAW 264.7 macrophages to low-intensity microwaves (MW). MATERIALS AND METHODS: Three inhibitors of TLR4, SAPK/JNK, and NF-κB signalling, namely CLI-095, SP600125, and IKK Inhibitor XII, respectively, were added to cultured RAW 264.7 macrophages before MW treatment. RESULTS: MW exposure resulted in stimulation of RAW 264.7 cell activity manifested by increases in cytokine production and the stimulation of cell signalling. The blocking of a key kinase of the NF-κB pathway by IKK Inhibitor XII resulted in decreased MW-induced TLR4 expression and increased SAPK/JNK and NF-κB phosphorylation in irradiated cells. In addition, IKK Inhibitor XII significantly decreased tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin 1α (IL-1α), interleukin 6 (IL-6), and interleukin 10 (IL-10) production in both exposed and unexposed RAW 264.7 macrophages. Inhibitor SP6000125 did not prevent an MW effect on signal proteins with the exception of decreased SAPK/JNK phosphorylation in RAW 264.7 cells. Cytokine production was markedly decreased in MW-exposed cells cultured with SP6000125. The inhibitor of TLR4, CLI-095, did not affect signal proteins and cytokine production changes in MW-exposed cells. CONCLUSIONS: The results suggest that low-intensity MW promotes macrophage activity via mechanisms involving cellular signalling, particularly the NF-κB pathway.

Promoter islands as a platform for interaction with nucleoid proteins and transcription factors.

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS--a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.

Inhibitors of TLR-4, NF-κB, and SAPK/JNK signaling reduce the toxic effect of lipopolysaccharide on RAW 264.7 cells.

The present study was designed to examine and compare the effects of three suppressors on the cytokine response in tandem with examining: the synthesis of inducible forms of heat shock proteins; HSP72 and HSP90α; activities of NF-κB and SAPK/JNK signaling pathways; and TLR4 expression. Pre-treatment with inhibitors offers promise as protective means to lower the activity of these cascades, thereby circumventing the formation of excessive amounts of pro-inflammatory molecules. Three inhibitors of TLR4, SAPK/JNK, and NF-κB signaling, namely CLI-095, SP600125, and IKK Inhibitor XII, respectively, were added to cultured RAW 264.7 macrophages before the Escherichia coli lipopolysaccharide (LPS) application. Treatments of RAW 264.7 cells with each of the inhibitors resulted in a reduced response to LPS as was visualized by a decrease of TNF-α, IL-1, and IFN-γ production. In addition, inhibitors of the NF-κB and SAPK/JNK signaling reduced IL-6 production in LPS-treated cells, whereas the IKK inhibitor XII also decreased IL-10 production. Further, the NO production in LPS-stimulated macrophages was significantly reduced following application of CLI-095 or IKK inhibitor XII. The results also showed that the inhibitors suppressed TLR4 production and decreased phosphorylation of NF-κB and SAPK/JNK proteins, thereby preventing the activation NF-κB and SAPK/JNK signaling pathways in LPS-activated cells. In addition, the production of inducible heat shock proteins, HSP72 and HSP90-α, was reduced in LPS-stimulated RAW 264.7 cells pre-treated with inhibitors. These results suggest that inhibitors CLI-095, SP600125, and IKK inhibitor XII demonstrate potential effectiveness in the reduction of the inflammatory response by mechanisms involving both the cellular defense system and cellular signaling. In conclusion, suppressor of NF-κB cascade, IKK inhibitor XII, seems to be the most effective anti-toxic agent among studied inhibitors.

Microarray with LNA-probes for genotyping of polymorphic variants of Gilbert's syndrome gene UGT1A1(TA)n.

BACKGROUND: Gilbert's syndrome is a common metabolic dysfunction characterized by elevated levels of unconjugated bilirubin in the bloodstream. This condition is usually caused by additional (TA) insertions in a promoter region of the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene, which instead of the sequence А(TА)6TАА contains А(TА)7TАА. While the condition itself is benign, it presents elevated risk for patients treated with irinotecan, a common chemotherapy drug. METHODS: The technique is based on hybridization analysis of a pre-amplified segment of the UGT1A1 gene promoter performed on a microarray. Specific probes containing locked nucleic acids (LNA) were designed and immobilized on the microarray to provide accurate identification. RESULTS: A microarray has been developed to identify both common and rare variants of UGT1A1(TA)n polymorphisms. In total, 108 individuals were genotyped. Out of these, 47 (43.5%) had homozygous wild-type genotypes (TA)6/(TA)6; 41(38%) were heterozygotes (TA)6/(TA)7; and 18 (16.7%)--homozygotes (TA)7/(TA)7. In two cases (1.8%), rare genotypes (TA)5/(TA)7 and (TA)5/(TA)6 were found. The results were in full agreement with the sequencing. In addition, synthetic fragments corresponding to all human allelic variants [(TA)5, (TA)6, (TA)7, (TA)8] were successfully tested. CONCLUSIONS: The developed microarray-based approach for identification of polymorphic variants of the UGT1A1 gene is a promising and reliable diagnostic tool that can be successfully implemented in clinical practice.

Gel-based microarrays in clinical diagnostics in Russia.

Immobilization of molecular probes in 3D hydrogel elements provides some essential advantages compared with conventional flat surfaces. In this article, an integrated technology based on the use of low-density microarrays comprised of hemispherical gel elements, developed at the Engelhardt Institute of Molecular Biology (Moscow, Russia) for various applications will be reviewed. The structure of the gel can be adapted for immobilization of virtually any biological molecules in a natural hydrophilic environment. The discrimination between matching and mismatching duplexes of nucleic acids in these conditions is more reliable than on conventional flat surfaces, minimizing the number of elements needed to detect specific sequences. Protein molecules immobilized in hydrogel-based biochips better preserve their biological properties. As described in this article, such biochips were successfully applied for laboratory diagnostics in a wide variety of clinical conditions involving the identification of bacterial and viral pathogens, cancer-related mutations and protein tumor markers.

Oligonucleotide microchip for subtyping of influenza A virus.

BACKGROUND: Influenza A viruses are classified into subtypes depending on the antigenic properties of their two outer glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Sixteen subtypes of HA and nine of NA are known. Lately, the circulation of some subtypes (H7N7, H5N1) has been closely watched because of the epidemiological threat they present. OBJECTIVES: This study assesses the potential of using gel-based microchip technology for fast and sensitive molecular subtyping of the influenza A virus. METHODS: The method employs a microchip of 3D gel-based elements containing immobilized probes. Segments of the HA and NA genes are amplified using multiplex RT-PCR and then hybridized with the microchip. RESULTS: The developed microchip was validated using a panel of 21 known reference strains of influenza virus. Selected strains represented different HA and NA subtypes derived from avian, swine and human hosts. The whole procedure takes 10 hours and enables one to identify 15 subtypes of HA and two subtypes of NA. Forty-one clinical samples isolated during the poultry fall in Novosibirsk (Russia, 2005) were successfully identified using the proposed technique. The sensitivity and specificity of the method were 76% and 100%, respectively, compared with the 'gold standard' techniques (virus isolation with following characterization by immunoassay). CONCLUSIONS: We conclude that the method of subtyping using gel-based microchips is a promising approach for fast detection and identification of influenza A, which may greatly improve its monitoring.