imagine (Institute of molecular genetics and genetic engineering)
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    De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance

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    Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydrationdesiccation.Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well asaccelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functionsalready one day upon watering [1].Aim: to obtain more insight into the mechanisms of desiccation tolerance in R. serbica by differential de novotranscriptomics of hydrated (HL) and desiccated leaves (DL).Abstract: [https://imagine.imgge.bg.ac.rs/handle/123456789/1834

    Comparative De Novo Transcriptomic Analysis of Photosynthetically Active and Non-Photosynthetically Active Tissues of Variegated Pelargonium zonale Leaves

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    Variegated Pelargonium zonale leaves have proven to be an excellent model system to examine source–sink interactions within the same organ providing the equal microenvironment conditions, unlike common shoot/ root relation studies. Photosynthetically non-active (W) mesophyll cells contain smaller plastids lacking thylakoid membranes or starch granules, and exhibit no peroxisomes in comparison to photosynthetically active (G) cells. With the aim of gaining a deeper insight into molecular phenotype of W leaf tissue, particularly the one related to photosynthetic-dependent H2O2 metabolism, transcriptomes of these two metabolically contrasted tissues were compared. High-quality total RNA from W and G leaf tissues was extracted according to our previously optimised protocol. Highly purified cDNA libraries were synthesized and sequenced on an Illumina platform. The ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed and the read quality was checked before and after the trimming. In total, 39763284 (with Q30=94.3%) and 42062153 (with Q30=94.0%) clean reads were obtained in G and W total RNA samples, respectively, and used to perform transcriptome assembly by Trinity software. After removing the redundancy, via Corset software, 139811 transcripts with 139575 unigenes were annotated through comparison with seven commonly used databases (NCBI non-redundant protein and nucleotide sequences; PFAM; Clusters of Orthologous Groups of proteins, Swiss-Prot, KEGG, GO). Analysis of differentially expressed genes was performed using DESeq2 R package and revealed 4668 upregulated genes and 6689 down-regulated genes in G tissue compared with W one. Among the up-regulated genes in G tissue, the majority was associated with cytoskeleton, photosynthetic processes, plastids, thylakoids and transport, while in W tissue up-regulated genes were mainly found to encode enzymes with ATPase activity, carbohydrate absorption and digestion, callose, pectin and linoleic acid metabolism. Moreover, a significant difference between these two tissues differing in H2O2 generation rate was observed in the expression level of genes involved in H2O2 scavenging. Enzymatic constituents of the ascorbate-glutathione cycle and glutathione-S-transferase were up-regulated in W tissue, while catalase, glutathione-peroxidases and three Class III peroxidases were all up-regulated in G tissue. The obtained transcriptome results were correlated with previously revealed morphological, biochemical, and molecular characteristics of these two tissues.Book of Abstracts: Belgrade BioInformatics Conference 202

    Brevibacillus laterosporus supplementation diet modulates honey bee microbiome

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    Among them, bacterial and fungal pathogens Paenibacillus larvae, Melissococcus pluton, Ascosphera apis and Nosema ceranae play a major impact on honey bees colonies. Thus, developing alternative prophylactic and curative strategies are urgently needed. The use of probiotic bacteria in honey bee supplemental feeding is therefore promising to treat or prevent diseases. Brevibacillus laterosporus, Gram-positive endospore forming bacilli, is recognised as one of the promising antibacterial and antifungal agents producer. The aim of this study was to examine the short-therm effects of B. laterosporus supplemented diet on worker honey bee microbiome. Dry spores of B. laterosporus strain BGSP11 have been administrated through a sugar syrup diet to ten colonies and a representative specimen of worker honey bees was taken before the start of the treatment and immediately after the syrup was consumed. The microbial diversity was assessed before and after the treatment using Illumina MiSeq sequencing platforms (ID Genomics service, Seattle, WA, USA). 16s rRNA sequencing for bacterial community profiling and fungal Internally Transcribes Spacer for mycological taxa profiling were used. The next-generation microbiome bioinformatics platform QIIME2 v 2021.4 was used for filtering and denoising obtained sequences, calculation of diversity metrics and taxonomy assignment. The feature classifier was trained using the Greengenes v 13_8 for bacterial taxa and fungal UNITE database v 8.3. The results obtained in this study indicated statisticaly significant alfa diversity between control and experimental group honey bee microbiota composition. The diversity abundance was higher in control comparing to the group treated with B. laterosporus strain BGSP11 spores. There was no significant diference in Bray- Curtis distance among two groups of analysed samples. Regarding to mycological abundance, composition was completely different between two groups; control group had Claviceps as predominant genus, while in treated group of honey bee microbiome Metschnikowia genus was prevalent, indicating that the presence of fungal pathogens in treated group is highly diminished.Book of Abstracts: Belgrade BioInformatics Conference 202

    Epigenetic mechanisms regulating the expression of human SOX3 gene and pluripotency factors (SOX2, OCT4, i NANOG) during the early stages of NTera2/D1 cells neural differentiation

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    ključne aktere u procesima održavanja pluripotentnosti, ćelijskog opredeljivanja i diferencijacije. Precizno koordinisana aktivnost ovih gena neophodna je za pravilan tok humane neuralne diferencijacije. U ovoj doktorskoj disertaciji analizirani su ekspresioni profili i epigenetički mehanizmi regulacije ekspresije pomenutih gena u ranim fazama neuralne diferencijacije NTeraT2/D1 ćelija indukovane retinoičnom kiselinom.U ovom model sistemu in vitro neuralne diferencijacije detektovane su dinamične izmene u ekspresionim profilima gena SOX1 i SOX3 i gena faktora pluripotentnosti (SOX2, OCT4 i NANOG) tokom ranih faza neuralne diferencijacije. Pokazano je da se ekspresija gena SOX1 i SOX3 aktivira odmah nakon indukcije neuralne diferencijacije ovih ćelija, čime je potvrđena njihova uloga ranih neuralnih markera. Ekspresija gena SOX2, OCT4 i NANOG, koji formiraju jezgro regulatorne mreže odgovorne za održavanje pluripotentnosti, smanjuje se tokom inicijacije neuralne diferencijacije i izlaska NTera2/D1 ćelija iz stanja pluripotentnosti na osnovu čega je zaključeno da signali koji indukuju neuralnu diferencijaciju već u početnim stadijumima dovode do intenzivnih promena u „molekularnom miljeu“ ćelije.U analizi epigenetičkih mehanizama uključenih u regulaciju ekspresije ispitivanih gena praćeni su metilacija DNK i dinamika izmene histonskih posttranslacionih modifikacija na njihovim regulatornim regionima, sa posebnim osvrtom na regulaciju ekspresije gena SOX3. Metodom metilacija-specifičnog PCR-a pokazano je da su promotori gena SOX1 i SOX3 hipometilovani kako u nediferenciranim NTera2/D1 ćelijama, tako i u ćelijama čija je neuralna diferencijacija indukovana retinoičnom kiselinom. Metodom bisulfitnog pirosekvenciranja DNK, koja predstavlja zlatni standard u merenju stepena metilacije, potvrđena je hipometilacija jednog od dva CpG ostrva u okviru promotora gena SOX3 čime je potvrđeno da metilacija DNK nije mehanizam regulacije ekspresije ovog gena u ranim fazama neuralne diferencijacije NTera2/D1 ćelija.Metodom hromatinske imunoprecipitacije analizirani su profili odabranih histonskih posttranslacionih modifikacija na regulatornim regionima gena SOX3 i SOX1 kao i gena faktora pluripotentnosti (SOX2, OCT4 i NANOG). Pokazano je da su izmene u depoziciji aktivirajućih histonskih markera H3K4me3 i H2B-acetil na regulatornim regionima gena SOX3 u korelaciji sa indukcijom ekspresije ovog gena u ranim fazama neuralne diferencijacije NTera2/D1 ćelija. Inicijacija neuralne diferencijacije praćena je smanjenjem prisustva H3K4me3 i H2B-acetil markerana promotoru gena SOX2, dok nijedna od analiziranih histonskih modifikacija nije u korelaciji sa detektovanim ekspresionim profilom gena SOX1...genes SOX1 and SOX3, together with pluripotency factors (SOX2, OCT4 and NANOG), have key roles in pluripotency maintenace, cell specification and differentiation and they act in a coordinate manner to regulate process of human neurogenesis. This doctoral disertation provides an insight into the expression profiles and epigenetic regulation of these genes during the early phases of retinoic acid-induced neural differentiation of NTera2/D1 cells.In this in vitro model system of human neurogenesis we have demontrated that expression profiles of SOX3 and SOX1 genes and pluripotency factors (SOX2, OCT4 i NANOG) are highly dynamic. It is shown that retinoic acid activates expression of SOX1 and SOX3, confirming their roles as early neural markers in vertebrates. Expression of SOX2, OCT4 and NANOG, which constitute core pluripotency regulatory circuitry, is reduced during the course of neural differentiation, suggesting that response to differentitation-inducing stimuli is followed by fast and intensive changes in cell transcriptome.For the analyses of epigenetic mechanisms acting on regulatory regions of SOX1 and SOX3 genes and pluripotency factors, DNA methylation and histone modifications profiles were examined, with special emphasis on SOX3 gene regulation. Using methylation-specific PCR it is shown that SOX1 and SOX3 gene promoters are hypomethylated in both undifferentiated NTera2/D1 cells and cells induced with retinoic acid. Bisulphite sequencing of the CpG island II in the promoter of SOX3 gene further confirmed that DNA methylation is not a mechanism governing regulation of SOX3 activity during the early stages of NTera2/D1 cell differentiation.Selected histone posttranslational modifications profiles on the regulatory regions of SOX1 and SOX3 genes and pluripotency factors were analyzed using chromatin immunoprecipitation. Changes in abundance of active H3K4me3 and H2B-acetyl marks on SOX3 regulatory regions are correlated with transcriptional activation of this gene. Furthermore, it is demonstrated that initiation of neural differentiation is accompanied by the decrease in H3K4me3 and H2B-acetyl marks on the promoter of SOX2 gene, while none of the analyzed histone modifications was correlated with previously detected SOX1 expression profile. In silico analyses demonstrated that histone profiles on the promoter regions of SOX1 and SOX3 genes in H1 human embryonal stem cells corresponds to bivalent genes with low transcriptional activity, while SOX2 gene promoter is enriched with activating histone marks. Obtained results have demonstrated important differences in the epigenetic mechanisms regulating the expression of SOXB1 family members, despite the existence of their functional redundancy..

    Nekodirajuće RNK kao perspektiva u dijagnostici i lečenju kardiovaskularnih bolesti

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    Kardiovaskularne bolesti (KVB) su klasa oboljenja koja obuhvataju srce i/ili krvne sudove i nastaju složenim sadejstvom genetičkih i stečenih faktora. Razvoj molekularne biologije omogućio je nove uvide u fundamentalne mehanizme koji dovode do KVB, kao i napredak u dijagnostici, prognostici i lečenju. Novi pristupi u dijagnostici i lečenju KVB podstaknuti su istraživanjima koja se odnose na nekodirajuće RNK - duge nekodirajuće RNK i kratke nekodirajuće RNK. Ova klasa molekula, ne samo da se povezuje sa različitim mehanizmima koji dovode do razvoja KVB, nego se prepoznaje njihov potencijal kao biomarkera, farmakogenetičkih faktora, novih meta lekova i novih alatki u lečenju bolesti. Upotreba nekih od njih u lečenju ljudi je i odobrena od strane relevantnih agencija. Posebnu pažnju privlače studije koje se odnose na nekodirajuće RNK poreklom iz ekstracelularnih vezikula, dodatno potvrđujući potencijal nekodirajuće RNK kao leka budućnosti, ne samo u tretmanu KVB.Cardiovascular diseases (CVDs) are group of diseases which encompass heart and/or blood vessels and they originate from complex coaction of genetic and acquired factors. Development of molecular biology has enabled new insights into fundamental mechanisms which lead to CVDs, as well as progress in diagnostics, prognosis and treatment. New approaches to diagnostics and treatment of CVDs have been encouraged by researches which are related to non-coding RNA, long non-coding and short non-coding RNA. Not only is this group of molecules being associated with different mechanisms which lead to CVDs, but their potential to be biomarkers, pharmacogenetic factors, new drug targets and new treatment tools is being recognised. Relevant agencies have approved some of them to be used for human treatments. Studies related to non-coding RNAs deriving from extracellular vesicles are getting special attention, additionally confirming non-coding RNAs potential as drug of the future, not limited just to CVDs

    De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance

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    Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydration-desiccation. Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well as accelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functions already one day upon watering [1]. The aim of our study was to obtain more insight into the desiccation tolerance mechanisms by differential de novo transcriptomics of hydrated (HL) and desiccated leaves (DL). For R. serbica transcriptome construction, the total high-quality RNA from HL and DL was extracted according to our previously optimised protocol [2]. Highly purified cDNA libraries were sequenced on an Illumina Hi-Seq platform. The ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed, and the quality of the reads was checked before and after the trimming. In total, 39608813 (with Q30=94%) and 37482969 (with Q30=94.1%) clean reads were obtained in HL and DL, respectively, and used to perform transcriptome assembly by Trinity software. After removing the redundancy, 189456 transcripts with 189003 unigenes were obtained (32.6% with the length between 500-1kbp).Comparative analysis revealed that a large portion of R. serbica sequences (49.1%) was similar to sequences found in the genome of another resurrection plant Boea hygrometrica. Furthermore, among obtained unigenes, 64.6% and 42.3% were annotated by NCBI non-redundant protein and nucleotide sequences database (db), 23% by PFAM db, 22.5% by Clusters of Orthologous Groups of proteins db, 48.02% by Swiss-Prot db, 23 % KEGG db and 13.73 by Gene Ontology db. The majority of annotated genes were associated with translation, ribosomal structure, posttranslational modifications, protein turnover, signalling pathways and cytoskeleton and encoded chaperonins and late embryogenesis abundant (LEA) proteins. Aiming to provide a list of candidates involved in the desiccation tolerance in R. serbica we analysed differentially expressed genes in HL and DL. Genes associated with transmembrane transport, reproduction, cell proliferation, and protein folding were up-regulated in HL compared with DL. On the other hand, genes encoding proteins involved in cell wall architecture, LEA proteins and antioxidative defence were up-regulated in DL.Book of Abstracts; Belgrade BioInformatics Conference 2021, 21-25 June 2021, Vinča, SerbiaPoster: [https://imagine.imgge.bg.ac.rs/handle/123456789/1855

    In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship

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    Desiccation or extreme water loss leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of hydrophilic, non-globular proteins is characterized by a high structural plasticity that allows them to adopt a random conformation in aqueous solutions that transforms into α-helices during dehydration [1]. Therefore, LEAPs can interact with various ligands and partners, including ion sequestration and stabilization of membranes and enzymes during freezing or drying [2]. Our new transcriptome database of an endemic resurrection species Ramonda serbica allowed us to identify 153 members of the LEA gene family. LEAPs of this sample data have an average primary sequence similarity and identity of 10% and 6%, respectively, but with a high variance (141 and 108), which means that the sample proteins can be classified based on domain homology. The averaging is based on multiple sequence alignment and the variance is estimated using pairwise sequence alignment scores. Accordingly, all identified LEAPs were clustered into six groups based on protein families (PFAM). Among these groups, LEAPs differ significantly in their secondary structure, disorder propensity and aggregation potential. Furthermore, we built homology models using Protein Data Bank structure information as templates. For each group, an ensemble of superimposed 3D homology models was analyzed. The information obtained from the representative structural models is key to understanding the function of LEAPs and the regulation of their intrinsic structural disorder-to-order transition during desiccation. This will pave the way for the identification of LEAPs endogenous partners and their targets in the cell and provide further insights into the protective mechanisms of desiccation tolerance.Related to poster: [https://imagine.imgge.bg.ac.rs/handle/123456789/1858

    Strukturna karakterizacija proteina zastupljenih u kasnoj fazi embriogeneze iz biljke Ramonda Serbica : Potencijalni inhibitor agregacije α‐ sinukleina

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    Ramonda serbica is an endemic and resurrection plant species that can survive extreme dehydration even over months. Desiccation (loss of >95% of cellular water) leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of anhydrobiosis-related intrinsically disordered proteins (IDPs) is characterized by high structural plasticity enabling them to interact with various ligands and partners, including ion sequestration and stabilization of membranes and enzymes during freezing or drying. the aim of our research is to assess the potential of selected RsLEAPs to inhibit the aggregation of α-synuclein, paving the way for new therapeutic strategies against neurodegenerative disorders, such as Parkinson’s disease. Our new transcriptome database of R. serbica leaves allowed us to identify around 165 members of LEA protein family. Based on multiple sequence alignment, secondary structure prediction and 3D structure modelling we classified identified LEAPs into six groups (according to the Pfam database) and showed that more than 50% of identified LEAPs exhibited a high propensity to form α-helices. As predicted by several bioinformatic tools, more than 70% of identified LEAPs were found to be highly disordered. By using molecular dynamic simulations, we identified the most favourable conformations of representative LEAPs and showed the loss of the secondary, α-helical structure in water, in contrast to globular proteins. Structural characterization of LEAPs is a key to understand their function and regulation of their intrinsic structural disorder-to-order transition during desiccation. These findings will promote transformative advancements in various fields, such as the development of new strategies in neurodegenerative disorders, cell preservation technology and the improvement of crop drought tolerance.Ramonda serbica endemska vrsta, i biljka vaskrsnica, sposobna da preživi u uslovima ekstremne dehidratacije tokom perioda dužeg od mesec dana. Desikacija (gubitak preko 95 % vode u ćeliji) dovodi do denaturacije, agregacije i degradacije proteina, i utiče na fluidnost membrana, što finalno dovodi do gubitka integriteta ćelije. Prisustvo proteina zastupljenih u kasnoj fazi embriogeneze (late embryogenesis abundant proteins – LEAPs) se smatra esencijalnim delom strategije tolerancije na desikaciju kod vaskrsnica. Ovu heterogenu grupu prirodno neuređenih proteina, povezanih sa anhidrobiozom, odlikuje visoka strukturna plastičnost koja im omogućava interakciju sa brojnim ligandima i partnerima. LEA proteini su uključeni u heliranje jona, stabilizaciju membrana i enzima tokom zamrzavanja ili suše. Cilj našeg istraživanja je procena potencijala izabranog LEA proteina iz ramonde da inhibira agregaciju α-sinukleina, otvarajući put ka razvoju novih terapija za lečenje neurodegenerativnih poremećaja poput Parkinskonove bolesti. Analiziranjem transkriptoma listova R. serbica i formiranjem baze podataka identifikovano je oko 165 proteina koji pripadaju LEA proteinskoj familiji. Na osnovu višestrukog poravnjanja aminokiselinskih sekvenci, predviđanja sekundarne strukture i 3D strukturnog modelinga, identifikovani LEA proteini su podeljeni u šest grupa (prema Pfam bazi podataka) i pokazano je sa velikom verovatnoćom da je više od 50 % LEA proteina u mogućnosti da formira α-helikse. Pomoću nekoliko bioinformatičkih alata predviđeno je da više od 70 % identifikovanih LEA proteina formira visoko neuređenu strukturu. Korišćenjem simulacije molekularne dinamike, identifikovane su najpovoljnije konformacije reprezentativnih LEA proteina. Tom prilikom je kod LEA proteina uočen gubitak sekundarne α-heliksne strukture u vodi, za razliku od globularnih proteina kada je ova struktura favorizovana. Strukturna karakterizacija LEA proteina je ključna za razumevanje njihove funkcije i regulaciju njihovog prelaska iz neuređene u uređenu konformaciju tokom desikacije. Ova saznanja bi trebalo da omoguće značajna napredovanja na različitim poljima, kao što je razvoj novih strategija u borbi protiv neurodegenerativnih poremećaja, tehnologija čuvanja zamrznutih ćelija, kao i na povećanje otpornosti useva na sušu

    Efficient production of highly purified Late Embryogenesis Abundant (LEA) protein from Arabidopsis thaliana by recombinant DNA technology

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    Late embryogenesis abundant (LEA) proteins are induced in cellular dehydration, such as freezing, drought, or desiccation. They can be involved in antioxidative defense, ion sequestration, and structural stabilization of both membranes and enzymes during freezing or drying, while by forming intracellular proteinaceous condensates they increase structural integrity and intracellular viscosity of cells during desiccation 1. The genome of the model plant Arabidopsis thaliana contains 51 genes encoding LEA proteins2. The majority of these LEA proteins (35%) belongs to Pfam LEA_4 (PF02987) family. In silico analysis suggested that these proteins are highly hydrophilic proteins with significant intrinsically disordered protein (IDP) properties. In order to evaluate structural properties and possible functions of LEA_4 protein family under different water content, a representative AtLEA25 protein (At2g42560, 635 aa), naturally located in the cytoplasm of seeds3 was obtained in Escherichia coli by recombinant DNA technology. Although this technology has been traditionally used to over-express and purify various globular proteins, numerous reports have shown that the IDPs, due to their structural plasicity are naturally highly susceptible to proteolytic cleavage. To conduct structural and functional studies we developed a robust method to produce highly purified (>95% pure) AtLEA25 with no detectable amount of protein breakdown products.Abstract: Serbian Biochemical Society, 10th Conference, Kragujevac, Serbia, 24.09.202

    The use of integrative multi-omics approach in cultivation and characterization of gut bacteria related to microbiota-gut-brain axis as a source for Next Generation Probiotics (NextGenBiotics)

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    The main idea of the NextGenBiotics is to cultivate novel Next Generation Probiotics (NGPs) related to microbiota-gut-brain axis (MGBA), in order to decipher their possible role in prevention and treatment of neurodegenerative and psychiatric diseases. Nearly one billion people suffer from neurodegenerative and 450 million people from a mental or behavioural disorders globally, with Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, autism spectrum disorder, and major depressive disorder as the most prevalent, representing a huge burden on society. Recently, all these diseases have been associated with the gut microbiota dysbiosis and alterations in MGBA functioning. The NextGenBiotics proposes a highly ambitious innovative multidisciplinary research strategy, with combination of traditional and cutting edge molecular microbiology methods including culturomics and integrative multi-omics approaches such as next generation sequencing, dual RNA seq transcriptomic analysis and metabolomics analysis as well as large-scale data sets analysis, coupled with in vitro and in vivo host-microbe interactions experiments. The pioneering work in NextGenBiotics will result in cultivation of novel anaerobic hitherto uncultivated and/or uncharacterized so far NGP strains and characterization of their effect on MGBA. The effects of selected NGPs on behaviour and neuronal activity will be revealed using C. elegans as well as the animal models for studying the MS and depression. Eventually, the results obtained during NextGenBiotics will beyond state- of-the-art help to determine the mechanisms involved in health-promoting effects of NGPs in MGBA, broadening the scientific knowledge and opening up the possible novel therapeutic approaches in prevention and therapy of neurodegenerative and psychiatric diseases in order to alleviate the disease symptoms and improve the quality of life.Principal Investigator: Dr Natasa Golic Duration period: 2021-2024Duration period: 2021-202

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