Biomarkers for personalised prevention of chronic diseases: a common protocol for three rapid scoping reviews.

INTRODUCTION: Personalised prevention aims to delay or avoid disease occurrence, progression, and recurrence of disease through the adoption of targeted interventions that consider the individual biological, including genetic data, environmental and behavioural characteristics, as well as the socio-cultural context. This protocol summarises the main features of a rapid scoping review to show the research landscape on biomarkers or a combination of biomarkers that may help to better identify subgroups of individuals with different risks of developing specific diseases in which specific preventive strategies could have an impact on clinical outcomes. This review is part of the "Personalised Prevention Roadmap for the future HEalThcare" (PROPHET) project, which seeks to highlight the gaps in current personalised preventive approaches, in order to develop a Strategic Research and Innovation Agenda for the European Union. OBJECTIVE: To systematically map and review the evidence of biomarkers that are available or under development in cancer, cardiovascular and neurodegenerative diseases that are or can be used for personalised prevention in the general population, in clinical or public health settings. METHODS: Three rapid scoping reviews are being conducted in parallel (February-June 2023), based on a common framework with some adjustments to suit each specific condition (cancer, cardiovascular or neurodegenerative diseases). Medline and Embase will be searched to identify publications between 2020 and 2023. To shorten the time frames, 10% of the papers will undergo screening by two reviewers and only English-language papers will be considered. The following information will be extracted by two reviewers from all the publications selected for inclusion: source type, citation details, country, inclusion/exclusion criteria (population, concept, context, type of evidence source), study methods, and key findings relevant to the review question/s. The selection criteria and the extraction sheet will be pre-tested. Relevant biomarkers for risk prediction and stratification will be recorded. Results will be presented graphically using an evidence map. INCLUSION CRITERIA: Population: general adult populations or adults from specific pre-defined high-risk subgroups; concept: all studies focusing on molecular, cellular, physiological, or imaging biomarkers used for individualised primary or secondary prevention of the diseases of interest; context: clinical or public health settings. SYSTEMATIC REVIEW REGISTRATION: https://doi.org/10.17605/OSF.IO/7JRWD (OSF registration DOI).

[Alternative Mechanisms of Mutagenesis at mCpG Sites during Replication and Repair].

5-Methyl-2'-deoxycytidine (mC) at CpG sites plays a key role in the epigenetic gene regulation, cell differentiation, and carcinogenesis. Despite the importance of mC for normal cell function, CpG dinucleotides are known as mutagenesis hotspots. Deamination of mC yields T, causing C→T transitions. However, several recent studies demonstrated the effect of epigenetic modifications of C on the fidelity and efficiency of DNA polymerases and excision repair enzymes. The review summarizes the available data that indicate the existence of deamination-independent mechanisms of mutagenesis at CpG sites.

Suppression of the Antioxidant System and PI3K/Akt/mTOR Signaling Pathway in Cisplatin-Resistant Cancer Cells by Quercetin.

We studied the effect of quercetin on ovarian adenocarcinoma SKOV-3 cell line and isogenic subline SKOV-3/CDDP resistant to the anticancer drug cisplatin. It was found that in resistant cells, quercetin in a concentration of 100 µM that causes a decrease in the cell viability suppressed the expression of genes encoding the key antioxidant enzymes (SOD2, CAT, GPX1, and HO-1), transcription factor Nrf2, and kinases of the PI3K/Akt/mTOR signaling pathway. In parental cells, quercetin, on the contrary, increased the expression of these genes. The results confirm the redox-dependent regulation induced by quercetin and its opposite nature in cisplatin-sensitive and cisplatin-resistant cancer cells.

Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L.

One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulation of development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologues of DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied. Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1), which contains all main structural domains required for catalytic activity. Using homologous modeling, we have constructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix- hairpin-helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA, and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand. The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower eff iciency, showing minimal activity in the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted in a global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein and other homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the status of epigenetic methylation and to control gene activity.

Suppression of PI3K/Akt/mTOR Signaling Pathway and Antioxidant System and Reversal of Cancer Cells Resistance to Cisplatin under the Effect of Curcumin.

The effect of curcumin on the resistance of SKOV-3 human ovarian adenocarcinoma cells to cisplatin was studied. It was found that curcumin induced "reversal" of cancer cells resistance, which was associated with suppression of the expression of genes encoding the key antioxidant enzymes (SOD1, SOD2, CAT, GPX1, and HO-1) and transcription factor Nrf2 and a decrease in the expression of genes encoding kinases of the PI3K/Akt/mTOR signaling pathway. The obtained results confirm the role of redox-dependent regulation in the "reversal" of cancer cells resistance to cisplatin.

[Template Properties of 5-Methyl-2'-Deoxycytidine and 5-Hydroxymethyl-2'-Deoxycytidine in Reactions with Human Translesion and Reparative DNA Polymerases].

5-Methyl-2'-deoxycytidine (mC) and the product of its controlled oxidation, 5-hydroxymethyl-2'-cytidine (hmC), play a key role in the epigenetic regulation of gene expression, the cell differentiation, and the carcinogenesis. Due to spontaneious deamination, genomic CpG sites containing mC and hmC serve as mutagenesis hotspots. In addition, error-prone translesion and reparative DNA polymerases may serve as additional source of mutations in the lesion-containing regions with CpG sites. In the present work, we performed in vitro analysis of the accuracy of nucleotide incorporation opposite to mC and hmC by human DNA polymerases Polß, Polλ, Polη, Polι, PoIκ and primase polymerase PrimPol. The results of the study show a high accuracy of copying mC and hmC by the reparative DNA polymerases polymerases Polß and Polλ, while Polη, Polι, PoIκ, and PrimPol copied mC and hmC with less accuracy evident by incorporation of dAMP and dTMP. The same spectrum of error-prone dNMP incorporation was also noted at sites with unmodified cytosines.

Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum.

A novel anaerobic, endospore-forming bacterium (strain M08 DMBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells of the strain were motile rods 1.3-2.0 µm long and 0.4 µm in diameter. The temperature range for growth was 5-42 °C, with an optimum at 30 °C. The pH range for growth was H 6.5-11.0, with an optimum at pH 8.0. Growth of strain M08 DMBT was observed at NaCl concentrations of 0-5.0 % (w/v) with an optimum at 1.0 %. Strain M08 DMBT utilized 3,4-dimethoxybenzoic acid, 2-methoxyphenol, carbon monoxide, glucose, fructose, mannose, xylose and yeast extract. The end product of glucose fermentation was acetate. The DNA G+C content of strain M08 DMBT was 32.3 mol% (obtained via whole genome sequencing). The closest phylogenetic relative of strain M08 DMBT was Alkalibaculum bacchi (family Eubacteriaceae, class Clostridia) with 95.17 % 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08 DMBT is considered to represent a novel species of the genus Alkalibaculum, for which the name Alkalibaculum sporogenes sp. nov. is proposed. The type strain of Alkalibaculum sporogenes is M08 DMBT (=KCTC 15840T=VKM B-3387T).

Ageing of Polymer Frictional Interfaces: The Role of Quantity and Quality of Contact.

When two objects are in contact, the force necessary for one to start sliding over the other is larger than the force necessary to keep the sliding motion going. This difference between static and dynamic friction is thought to result from a reduction in the area of real contact upon the onset of slip. Here, we resolve the structure in the area of contact on the molecular scale by means of environment-sensitive molecular rotors using (super-resolution) fluorescence microscopy and fluorescence lifetime imaging. We demonstrate that the macroscopic friction force is not only controlled by the area of real contact but also controlled by the "quality" of that area of real contact, which determines the friction per unit contact area. We show that the latter is affected by the local density of the contacting surfaces, a parameter that can be expected to change in time at any interface that involves glassy, amorphous materials.

Quality of Preovulatory (GV) Oocytes in Mice after Injection of eCG at Various Stages of the Estrous Cycle.

We studied the influence of the estrous cycle on the morphology of preovulatory (germinal vesicle, GV) oocytes in mice and their capacity to meiotic maturation in vitro. After standard injections of eCG gonadotropin (PMSG, Follimag) to females at different stages of the estrous cycle, the maximum levels of GV oocytes (26±1/mouse) were isolated from the ovaries of animals injected with the hormone during estrus. The capacity of isolated GV oocytes to meiotic maturation in vitro decreased in the following order: estrus (75.5±2.3%), metestrus (67.9±3.4%), proestrus (57.8±4.4%), and diestrus (50.6±5.6%); the differences between estrus and diestrus/proestrus were significant (p<0.05). After eCG injections during estrus, GV oocytes differed from other oocytes by lesser total diameter, lesser diameter of cytoplasm, lesser thickness of zona pellucida, and moderately dilated perivitelline space. These signs reflected higher competence of the "estrous" GV oocytes for meiotic maturation in vitro. Hormone stimulation of females with eCG, with consideration for the stage of the estrous cycle, seems to be an effective method for improving the quality of GV oocytes isolated from mouse ovaries.

Comparative Analysis of Number and Competence in Meiotic Maturation of Preovulatory Oocytes of C57Bl/6J Mice and Their F1 Hybrids after Stimulation with Gonadotropin.

The study examined maturation of preovulatory germinal vesicles oocytes (GV oocytes) induced by gonadotropic hormone PMSG in the inbred C57Bl/6J mice (viewed as a gold standard for diverse biomedical studies) as well as in the first generation hybrid C57Bl/6J×СВА/lac and СВА/lac×C57Bl/6J mice at various ages. The most effective donors of GV oocytes were СВА/lac×C57Bl/6J mice (F1 hybrids) yielding 25±2 oocyte/mouse. In contrast, a significantly smaller number of GV oocytes can be isolated from the ovaries of female C57Bl/6J or C57Bl/6J×СВА/lac mice under the same conditions. At this, the greatest number of GV oocytes (42±4) can be retrieved from the ovaries of immature hybrid СВА/lac×C57Bl/6J mice aged 4 weeks. These mice demonstrated the largest share of GV oocytes, which attained MII stage during in vitro culturing. The data conclude that F1 hybrid СВА/lac×C57Bl/6J mice can be viewed as a handy experimental source yielding a large number of GV oocytes capable of meiotic maturation in a culture.

Vestibular function in panic disorder patients: a vestibular-evoked myogenic potentials and video head impulse test study.

PURPOSE: To evaluate the function of the utriculus and sacculus and their central connections by ocular and cervical vestibular-evoked myogenic potentials (oVEMPs and cVEMPs), and the function of high-frequency VOR of the semicircular canals by video head impulse test (vHIT) in patients with panic disorder (PD). METHODS: Forty-eight patients with PD (21 with agoraphobia) and 20 sex- and age-matched healthy controls took part in the investigation. The vestibulo-ocular reflex (VOR) gains and latencies and peak-to-peak amplitudes of sound-induced VEMPs were measured and compared with those of healthy controls. RESULTS: Any statistical differences in the parameters of cVEMP and oVEMP responses between both PD patients groups and between patients and healthy controls were not observed. Also, significant differences between VOR in patients and healthy controls were not found. The VOR gain, bilaterally in the three semicircular canals was within normal limits (0.8-1.2) for 67%, and higher for 33% of the patients with PD. Overt and covert saccades were not observed. The relationship between higher VOR gains and the increase of postural instability when a sensory conflict exists (standing on foam pad with eyes closed) for patients with PD was established. CONCLUSION: The VEMPs and vHIT tests demonstrated that there is no evidence of hypofunction of the semicircular canals in the high-frequency spectrum of VOR functioning. Nor are there any indications of impairment of the otolith system in patients with PD, regardless of their subjective vestibular sensations. The findings of the current study confirm the proposed link between anxiety, panic symptoms and postural instability in PD patients.

Patient, tumor, and healthcare factors associated with regional variability in lung cancer survival: a Spanish high-resolution population-based study.

PURPOSE: The third most frequently diagnosed cancer in Europe in 2018 was lung cancer; it is also the leading cause of cancer death in Europe. We studied patient and tumor characteristics, and patterns of healthcare provision explaining regional variability in lung cancer survival in southern Spain. METHODS: A population-based cohort study included all 1196 incident first invasive primary lung cancer (C33-C34 according to ICD-10) cases diagnosed between 2010 and 2011 with follow-up until April 2015. Data were drawn from local population-based cancer registries and patients' hospital medical records from all public and private hospitals from two regions in southern Spain. RESULTS: There was evidence of regional differences in lung cancer late diagnosis (58% stage IV in Granada vs. 65% in Huelva, p value < 0.001). Among patients with stage I, only 67% received surgery compared with 0.6% of patients with stage IV. Patients treated with a combination of radiotherapy, chemotherapy, and surgery had a 2-year mortality risk reduction of 94% compared with patients who did not receive any treatment (excess mortality risk 0.06; 95% CI 0.02-0.16). Geographical differences in survival were observed between the two regions: 35% vs. 26% at 1-year since diagnosis. CONCLUSIONS: The observed geographic differences in survival between regions are due in part to the late cancer diagnosis which determines the use of less effective therapeutic options. Results from our study justify the need for promoting lung cancer early detection strategies and the harmonization of the best practice in lung cancer management and treatment.

Neuroanatomical variations as a function of experience in a complex daily task: A VBM and DTI study on driving experience.

Complex tasks require the learning and integration of multiple cognitive, sensory, and psychomotor skills for correct execution. Driving-related skills are developed step by step through the increase of mileage driven and the accumulation of practice in different traffic situations. The acquisition of these skills should be reflected in the brain structure. However, no previous studies have explored brain structural variations associated with driving experience. The aim of the present study was to investigate whether driving frequency, defined as average annual driving mileage, is related to neuroanatomical variations in gray matter (GM) volume and white matter (WM) integrity using voxel-based morphometry (VBM) and DTI-based fractional anisotropy (FA), respectively. We recruited 83 drivers with variable range of annual driving mileage and controlled for age, sex, handedness, IQ, time since the acquisition of driving license, use of motorcycles/mopeds and bicycles, perceived driving skills, and subjective probability of having an accident. Our results showed variations in white matter FA as a function of mileage driven. Driving experience was related to a significant increase of FA in parts of the right hemisphere superior and inferior longitudinal fasciculus, anterior thalamic radiation, forceps majors, inferior fronto-occipital fasciculus, and corticospinal tract. No significant differences were observed in gray matter volumes. FA variations were found in brain regions that have been associated with cognitive, visual, and motor processes necessary for skilled performance in driving. These results suggest that variations in white matter diffusivity can underlie the development of driving skills and safer driving.

[Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].

Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and ß-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons.

[New strains of basidiomycetes that produce bioethanol from lignocellulose biomass].

Sixty six isolates were screened for ability of bioethanol production; dynamics of product accumulation and substrate utilization were investigated for two selected strains Trametes hirsuta MT-24.24 and Trametes versicolor IT-1. The strains' efficiency was evaluated as bioethanol production by 1 g biomass. Strain T. versicolor IT-1 producing over 33 g/L of the ethanol for 9 d was selected. Direct conversion of Na-carboxymethyl cellulose, microcrystalline cellulose and straw was shown with ethanol yields of 2.1, 1.6 and 1.7 g/L, respectively, for 9 d fermentation time.

Unique configuration of genes of silicon transporter in the freshwater pennate diatom Synedra acus subsp. radians.

The existence of the cluster of duplicated sit silicon transporter genes in the chromosome of the diatom Synedra acus subsp. radians was shown for the first time. Earlier, the localization of sit genes in the same chromosome and cluster formation caused by gene duplication was shown only for the marine raphid pennate diatom P. tricornutum. Only non-clustered sit genes were found in the genomes of other diatoms. It is reasonable to assume that sit tandem (sit-td) and sit triplet (sit-tri) genes of S. acus subsp. radians occurred as a result of gene duplication followed by divergence of gene copies.

Sequencing of the complete genome of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal.

High-throughput method of sequencing was applied to determine the complete nucleotide sequence of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal (East Siberia). The assembled genome has a total length of 98 Mbp, the mean coverage is 33x. Structure-functional annotation of the genome was performed.

Similarity of structure of taxonomic bacterial communities in the photic layer of Lake Baikal's three basins differing in spring phytoplankton composition and abundance.

Pyrosequencing of amplicons V3-V4 of the 16S rRNA gene of 30 samples from the photic layer across the three basins of Lake Baikal has revealed 44 958 sequences of the domain Bacteria. The most representative phylums among all classified sequences in the samples were Actinobacteria, Bacteroidetes, Verrucomicrobia, Proteobacteria, Acidobacteria, and Cyanobacteria. As much as 38.5% of the total number of sequences has been determined to the level of genus. The taxonomic composition of bacterial communities was similar regardless of some differences in the composition and abundance of spring phytoplankton. Closely related or identical sequences of bacteria inhabiting the epilimnion of other lakes worldwide have been discovered for most sequences. This confirms the similarity of microbial communities in freshwater ecosystems.