imagine (Institute of molecular genetics and genetic engineering)
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Supporting information: Pantelic, B., Skaro Bogojevic, S., Milivojevic, D., Ilic-Tomic, T., Lončarević, B., Beskoski, V., Maslak, V., Guzik, M., Makryniotis, K., Taxeidis, G., Siaperas, R., Topakas, E., & Nikodinovic-Runic, J. (2023). Set of Small Molecule Polyurethane (PU) Model Substrates: Ecotoxicity Evaluation and Identification of PU Degrading Biocatalysts. Catalysts, 13(2), Art. 2. https://doi.org/10.3390/catal13020278
Get PDFPublished version: [https://imagine.imgge.bg.ac.rs/handle/123456789/1790]Supplementary material for: [ https://doi.org/10.3390/catal13020278
Integrative transcriptomic and TMT-based proteomic analysis reveals the desiccation tolerance in Ramonda serbica Panc.
Get PDFRamonda serbica Panc. is a resurrection plant that can survive long periods of desiccation and
fully restores its metabolic functions just one day after watering. The aim of this study was to
identify key candidates and metabolic pathways involved in R. serbica desiccation tolerance.
We combined differential transcriptomics and proteomics with the analysis of phenolics,
sugars, cell wall polymers and photosynthetic electron transport (PET) chain. TMT-based
proteomic analysis allowed the relative quantification of 1192 different protein groups, 408 of
which were differentially abundant between hydrated (HL) and desiccated leaves (DL). Almost
all differentially abundant proteins and transcripts related to photosynthetic processes were
downregulated in DL. Chlorophyll fluorescence measurements showed a shift from linear PET
to cyclic electron transport (CET). The levels of H2O2-scavenging enzymes, ascorbate-
glutathione cycle components, catalases, peroxiredoxins, Fe-, and Mn superoxide dismutase
(SOD) were reduced in DL. However, six germin-like proteins (GLPs), four Cu/ZnSOD
isoforms, three polyphenol oxidases, and 22 late embryogenesis abundant proteins (LEAPs;
mainly LEA4 and dehydrins), were desiccation-inducible. Desiccation led to cell wall
remodelling related to GLP-derived H2O2/HO●
activity and pectin demethylesterification. This
comprehensive study contributes to understanding the role and regulation of important
metabolic pathways during desiccation with the final aim to help improving the drought
tolerance in crops.Abstract: 5th Conference of the International Plant Proteomics Organization; May 22-25, 2022 | Porto Palace Hotel | Thessaloniki, Hella
CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response
Get PDFGlobal climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress respons
Molecular profiling of rare thymoma using next-generation sequencing: meta-analysis
Get PDFAbstractBackgroundThymomas belong to rare tumors giving rise to thymic epithelial tissue. There is a classification of several forms of thymoma: A, AB, B1, B2, B3, thymic carcinoma (TC) and thymic neuroendocrine thymoma. In this meta-analysis study, we have focused on thymoma using articles based on the disease’s next-generation sequencing (NGS) genomic profiling.Materials and methodsWe conducted a systematic review and meta-analysis of the prevalence of studies that discovered the genes and variants occurring in the less aggressive forms of the thymic epithelial tumors. Studies published before 12th December 2022 were identified through PubMed, Web of Science (WoS), and SCOPUS databases. Two reviewers have searched for the bases and selected the articles for the final analysis, based on well-defined exclusion and inclusion criteria.ResultsFinally, 12 publications were included in the qualitative as well as quantitative analysis. The three genes, GTF2I, TP53, and HRAS, emerged as disease-significant in the observed studies. The Odds Ratio for all three extracted genes GTF2I (OR = 1.58, CI [1.51, 1.66] p < 0.00001), TP53 (OR = 1.36, CI [1.12, 1.65], p < 0.002), and HRAS (OR = 1.02, CI [1.00, 1.04], p < 0.001).ConclusionsAccording to obtained data, we noticed that the GTF2I gene exhibits a significant prevalence i
Translating Bioinformatics Back To Healthcare: Facilitating the use of Artificial Intelligence at UW Medicine
Get PDFIt is an opportune time to be engaged in the research and application of informatics
in biomedicine. The increased use of electronic and personal health records and
personal mobile devices is creating many opportunities at research academic medical
centers. At the University of Washington, I believe we are laying the groundwork to
build the informatics and information technology infrastructure to support research on
personalized approaches and the use of data science to enable them. We are beginning
to see the early successes of these efforts and I will describe some of them. But there are
many challenges, for example, we continue to generate massive amounts of data that is
largely uncurated. This includes images, genomes and other -omics datasets, personal
monitors, electronic health records, etc. In this presentation, I will discuss our support of
data for research use within UW Medicine, our efforts to build new machine learning and
data science approaches using clinical datasets, and our efforts to develop new machine
learning methods and to implement them so that we can study the impacts of their use.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Prediction of cell types using single-cell mRNA profiles
Get PDFSingle cell transcriptomics is a rapidly growing area with an urgent need for new analytical
tools to complement and supersede unsupervised clustering. We defined a new method
for deriving gene expression profiles from single-cell gene expression matrices. We
named these profiles the “single-cell-derived-class” (SCDC) profiles. We developed SCDC
profiles for multiple cell types and subtypes of peripheral blood mononuclear cells (PBMC)
using the results of single cell transcriptomics (SCT) experiments. SCDC profiles represent
characteristic patterns of gene expressions of the types and subtypes of healthy human
PBMC. We studied the reproducibility of SCDC profiles, their robustness, and their
applications in classifying healthy human PBMC types and subtypes. SCDC profiles are
efficient and convenient tools for the analysis of SCT data derived from PBMC samples.
These profiles are highly reproducible, even when derived from unrelated studies,
provided that the sample processing steps are comparable and the same SCT technology
is used. The classification accuracy of SCDC profiles is high. SCDC profiles can be used for
supervised classification and the discovery of new subtypes of PBMC.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
AI-powered framework to predict the toxicity of microplastics
Get PDFNumerous articles have been published investigating the health effects of exposure
to micro- and nanoplastics (MNPs). However, these studies have yielded inconclusive
findings due to the lack of comparability between them and the complex and diverse
nature of the existing toxicity data on MNPs. This study presents a predictive modeling
framework for assessing the cytotoxicity of MNPs using machine learning techniques
based on classification. Through a thorough literature search, a dataset comprising
1824 sample points was compiled, incorporating nine features that describe the
physicochemical properties of MNPs, cell-related attributes, and experimental factors.
The decision tree ensemble classifier constructed using all the features (referred to as
DTE1) exhibited a high predictive accuracy of 0.95, along with a recall and precision of 0.86
each. To identify the key factors influencing the toxic properties of MNPs, feature selection
was performed. A simplified classifier utilizing six influential features demonstrated a
comparable performance to DTE1. These findings can guide future studies by improving
experimental design and reporting practices, ultimately enhancing our understanding of
the urgent health concerns related to MNPs. As more representative research data is
incorporated, the developed model holds the potential for broad applicability in various
settings concerning MNP cytotoxicity.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
A novel Bacillus subtilis BPM12 with high bis(2 hydroxyethyl)terephthalate hydrolytic activity efficiently interacts with virgin and mechanically recycled polyethylene terephthalate
Get PDFBiotechnological treatment of plastic waste has gathered substantial attention as an efficient and generally greener approach for polyethylene terephthalate (PET) depolymerization and upcycling in comparison to mechanical and chemical processes. Nevertheless, a suitable combination of mechanical and microbial degradation may be the key to bringing forward PET upcycling. In this study, a new strain with an excellent bis(2 hydroxyethyl)terephthalate (BHET) degradation potential (1000 mg/mL in 120 h at 30 °C) and wide temperature (20-47 °C) and pH (5-10) tolerance was isolated from a pristine soil sample. It was identified as Bacillus subtilis BPM12 via phenotypical and genome analysis. A number of enzymes with potential polymer degrading activities were identified, including carboxylesterase BPM12CE that was efficiently expressed both, homologously in B. subtilis BPM12 and heterologously in B. subtilis 168 strain. Overexpression of this enzyme enabled B. subtilis 168 to degrade BHET, while the activity of BPM12 increased up to 1.8-fold, confirming its BHET-ase activity. Interaction of B. subtilis BPM12 with virgin PET films and films that were re-extruded up to 5 times mimicking mechanical recycling, revealed the ability of the strain to attach and form biofilm on each surface. Mechanical recycling resulted in PET materials that are more susceptible to chemical hydrolysis, however only slight differences were detected in biological degradation when BPM12 whole-cells or cell-free enzyme preparations were used. Mixed mechano/bio-degradation with whole-cells and crude enzyme mixes from this strain can serve to further increase the percentage of PET- based plastics that can enter circularity
De novo Genome Assembly of Sweet Chestnut (Castanea sativa Mill.) Insights into the Molecular Basis of its Nutritional Properties
Get PDFThe Sweet Chestnut (Castanea sativa Mill.) is a tree species that holds significant economic
importance and naturally spreads throughout central-southern Europe and Asia Minor. Its
highly nutritious nuts have a unique composition that sets them apart from other nuts,
being rich in vitamins, including vitamin C, and B vitamins such as thiamine, niacin, and
folate. Over the last few decades, breeding efforts have prioritized the development of
sweet chestnut cultivars that are resistant to blight and produce better nuts. However,
despite these efforts, molecular genetic studies of the sweet chestnut have been
insufficient. To bridge this knowledge gap, we set out to create the first reference genome
of the sweet chestnut using whole-genome shotgun paired-end sequencing. Our study
involved genome-wide analyses to identify and functionally annotate genes in sweet
chestnut, and develop and confirm SSR-SNP markers. Additionally, we have identified
and characterized specific genomic loci that enhance the nutritional value of sweet
chestnuts. To the best of our knowledge, this is the first study to investigate the genetic
loci responsible for determining the nutritional value of chestnuts. We anticipate that our
findings will significantly contribute to the development of sweet chestnut cultivars with
higher levels of bioactive compounds, minerals, and digestibility, ultimately enhancing the
nutritional value of chestnuts.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Two-Step Upcycling Process of Lignocellulose into Edible Bacterial Nanocellulose with Black Raspberry Extract as an Active Ingredient
Get PDFBackground: Bacterial nanocellulose (BNC) has gained in popularity over the years due to its outstanding properties such as renewability, biocompatibility, and bioavailability, and its use as an eco-friendly material of the future for replacing petrochemical products. (2) Methods: This research refers to the utilization of lignocellulose coming from wood waste via enzymatic hydrolysis to produce biopolymer BNC with an accumulation rate of 0.09 mg/mL/day. Besides its significant contribution to the sustainability, circularity, and valorization of biomass products, the obtained BNC was functionalized through the adsorption of black raspberry extract (BR) by simple soaking. (3) Results: BR contained 77.25 ± 0.23 mg GAE/g of total phenolics and 27.42 ± 0.32 mg CGE/g of total anthocyanins. The antioxidant and antimicrobial activity of BR was evaluated by DPPH (60.51 ± 0.18 µg/mL) and FRAP (1.66 ± 0.03 mmol Fe2+/g) and using a standard disc diffusion assay, respectively. The successful synthesis and interactions between BNC and BR were confirmed by FTIR analysis, while the morphology of the new nutrient-enriched material was investigated by SEM analysis. Moreover, the in vitro release kinetics of a main active compound (cyanidin-3-O-rutinoside) was tested in different release media. (4) Conclusions: The upcycling process of lignocellulose into enriched BNC has been demonstrated. All findings emphasize the potential of BNC–BR as a sustainable food industry material